Yes / Bacterial cells sense their population density and respond accordingly by producing various signal molecules to the surrounding environments thereby trigger a plethora of gene expression. This regulatory pathway is termed quorum sensing (QS). Plenty of bacterial virulence factors are controlled by QS or QS-mediated regulatory systems and QS signal molecules (QSSMs) play crucial roles in bacterial signaling transduction. Moreover, bacterial QSSMs were shown to interfere with host cell signaling and modulate host immune responses. QSSMs not only regulate the expression of bacterial virulence factors but themselves act in the modulation of host biology that can be potential therapeutic targets. / Open Access Funding from the University of Dundee.Also supported by the University of Malaya High Impact Research Grants (UMC/625/1/HIR/MOHE/CHAN/01,A-000001-50001,and UM C/625/1/HIR/MOHE/CHAN/14/1, H-50001-A000027)

Yes / Bacteria sense their own population size, tune the expression of responding genes, and behave accordingly to environmental stimuli by secreting signaling molecules. This phenomenon is termed as quorum sensing (QS). By exogenously manipulating the signal transduction bacterial population behaviors could be controlled, which may be done through quorum quenching (QQ). QS related regulatory networks have been proven their involvement in regulating many virulence determinants in pathogenic bacteria in the course of infections. Interfering with QS signaling system could be a novel strategy against bacterial infections and therefore requires more understanding of their fundamental mechanisms. Here we review the development of studies specifically on the inhibition of production of N-acyl-homoserine lactone (AHL), a common proteobacterial QS signal. The opportunistic pathogen, Pseudomonas aeruginosa, equips the alkylquinolone (AQ)-mediated QS which also plays crucial roles in its pathogenicity. The studies in QQ targeting on AQ are also discussed. / University of Malaya High Impact Research Grants (UMC/625/1/HIR/MOHE/CHAN/01, A-000001-50001,and UMC/625/1/HIR/MOHE/CHAN/14/1, H-50001-A000027)

Yes / Dickeya sp. strain 2B12 was isolated from a freshwater lake in Malaysia. Here, we report the draft genome sequence of Dickeya sp. 2B12 sequenced by the Illumina MiSeq platform. With the genome sequence available, this genome sequence will be useful for the study of quorum-sensing activity in this isolate. / University of Malaya High-Impact Research( HIR)grants(UMC/625/1/HIR/MOHE/CHAN/01[no.A-000001- 50001] and UM-MOHE HIR UM C/625/1/HIR/MOHE/CHAN/14/1 [no. H-50001-A000027])

Yes / Burkholderia spp. rely on N-acyl homoserine lactone as quorum-sensing signal molecules which coordinate their phenotype at the population level. In this work, we present the whole genome of Burkholderia sp. strain A9, which enables the discovery of its N-acyl homoserine lactone synthase gene. / UM High Impact Research Grants (UM-MOHE HIR grant UM C/625/1/HIR/MOHE/CHAN/01, H-50001-A000001 and UMMOHE HIR Grant UM C/625/1/HIR/MOHE/CHAN/14/1, H-50001- A000027)

Yes / Aeromonas hydrophila has emerged worldwide as a human pathogen. Here, we report the draft whole-genome sequence of a freshwater isolate from Malaysia, A. hydrophila strain M062, and its N-acylhomoserine lactone genes are also reported here. / University of Malaya via High-Impact Research Grants (UM C/625/1/HIR/MOHE/CHAN/01, no. A-000001- 50001), and aUM-MOHEHIR grant (UM C/625/1/HIR/MOHE/CHAN/ 14/1, no. H-50001-A000027)

Yes / Lysinibacillus fusiformis strain RB21 is a quorum-quenching bacterium that is able to degrade quorum-sensing signaling molecules. Here, we present the first complete genome sequence of L. fusiformis strain RB21. The finished genome is 4.8 Mbp in size, and the quorum-quenching gene was identified. / University of Malaya for High Impact Research (UM-MOHE HIR) grant UM C/625/1/HIR/MOHE/CHAN/01, no. A000001-50001 and grant UM C/625/1/HIR/MOHE/CHAN/14/1, H-50001-A000027

Yes / We report the draft genome sequence of Pandoraea sp. strain E26 isolated from a former landfill site, sequenced by the Illumina MiSeq platform. This genome sequence will be useful to further understand the quorum-sensing system of this isolate. / University of Malaya High-Impact Research (HIR) grants (UM C/625/1/HIR/MOHE/CHAN/01, grant A-000001- 50001 and UM-MOHE HIR UM C/625/1/HIR/MOHE/CHAN/14/1, grant H-50001-A000027)

O Cancro Cítrico, um dos mais graves problemas fitossanitários da citricultura atual, é uma doença causada pelo fitopatógeno Xanthomonas axonopodis pv. citri (Xac). Um estudo funcional do genoma de Xac foi iniciado com o intuito de identificar interações proteína-proteína envolvidas em processos de patogenicidade de Xac. Através da utilização do sistema duplo-híbrido de levedura, baseado nos domínios de ligação ao DNA e ativação da transcrição do GAL4, nós analisamos os principais componentes dos mecanismos de patogenicidade de Xac, incluindo o Sistema de Secreção do Tipo III (TTSS), Sistema de Secreção do Tipo IV (TFSS) e Sistema de \"Quorum Sensing\" composto pelas proteínas Rpf. Componentes desses sistemas foram utilizados como iscas na triagem de uma biblioteca genômica de Xac. O TTSS é codificado pelos genes denominados hrp (\"hypersensitive response and pathogenicity\"), hrc (\"hrp conserved\") e hpa (\"hrp associated\") localizados no locus hrp do cromossomo de Xac. Esse sistema de secreção é capaz de translocar proteínas efetoras do citoplasma bacteriano para o interior da célula hospedeira. Nossos resultados mostraram novas interações proteínaproteína entre componentes do próprio TTSS além de associações específicas com uma proteína hipotética: 1) HrpG, um regulador de resposta de um sistema de dois componentes responsável pela expressão dos genes hrp, e XAC0095, uma proteína hipotética encontrada apenas em Xanthomonas spp; 2) HpaA, uma proteína secretada pelo TTSS, HpaB e o domínio C-terminal da HrcV; 3) HrpB1, HrpD6 e HrpW, 4) HrpB2 e HrcU e 5) interações homotrópicas envolvendo a ATPase HrcN. Em Xac, foram encontrados dois loci vir que codificam proteínas que possuem similaridade com componentes do TFSS envolvido em processos de conjugação/secreção bacteriana: TFSS-plasmídeo localizado no plasmídeo pXAC64 e TFSS-cromossomo localizado no cromossomo de Xac. O TFSS-plasmídeo, o qual possui maior similaridade com sistemas de conjugação, mostrou interações envolvendo proteínas cujos genes estão localizados na mesma região do plasmídeo pXAC64: 1) interação homotrópica da TrwA; 2) XACb0032 e XACb0033; 3) interações homotrópicas da proteína XACb0035; 4) VirB1 e VirB9; 5) XACb0042 e VirB6; 6) XACb0043 e XACb0021b. O TFSS-cromossomo apresentou interações envolvendo as proteínas: 1) VirD4 e um grupo de 12 proteínas que contém similaridade entre si, incluindo XAC2609 cujo gene encontra-se no locus vir, 2) XAC2609 e XAC2610; 3) Interações homotrópicas da VirB11; 4) XAC2622 e VirB9. A análise do sistema de \"Quorum-Sensing\" composto pelas proteínas Rpf mostrou interações envolvendo componentes do próprio sistema: 1) RpfC e RpfF; 2) RpfC e RpfG; 3) interações homotrópicas da RpfF; 4) RpfC e CmfA, uma proteína similar a Cmf de Dictyostelium discoideum que, neste organismo, é fundamental para processos de \"quorum-sensing\". As interações proteína-proteína encontradas permitiram-nos entender melhor a composição, organização e regulação dos fatores envolvidos na patogenicidade de Xac. / Citrus Canker, caused by the bacterial plant pathogen Xanthomonas axonopodis pv. citri (Xac) presents one of the most serious problems to Brazilian citriculture. We have initiated a project to identify protein-protein interactions involved in pathogenicity of Xac. Using a yeast two-hybrid system based on GAL4 DNA-binding and activation domains, we have focused on identifying interactions involving subunits, regulators and substrates of: Type Three Secretion System (TTSS), Type Four Secretion System (TFSS) and Quorum Sensing/Rpf System. Components of these systems were used as baits to screening a random Xac genomic library. The TTSS is coded by the hrp (hypersensitive response and pathogenicity), hrc (hrp conserved) and hpa (hrp associated) genes in the chromosomal hrp locus. This secretion system can translocate efector proteins from the bacterial cytoplasm into the host cells. We have identified several previously uncharacterized interactions involving: 1) HrpG, a two-component system response regulator responsible for the expression of Xac hrp operons, and XAC0095, a previously uncharacterized protein encountered only in Xanthomonas spp; 2) HpaA, a protein secreted by the TTSS, HpaB and the C-terminal domain HrcV; 3) HrpB1, HrpD6 and HrpW; 4) HrpB2 and HrcU; 5) Homotropic interactions were also identified for the ATPase HrcN. Xac contains two virB gene clusters, one on the chromosome and one on the pXAC64 plasmid, each of which codes for a unique and previously uncharacterized TFSS. Components of the TFSS of pXAC64, which is most similar to conjugation systems, showed interactions involving proteins coded by the same locus: 1) Homotropic interactions of TrwA; 2) XACb0032 and XACb0033; 3) XAC0035 homotropic interactions; 4) VirB1 and VirB9; 5) XACb0042 and VirB6; 6) XACb0043 and XACb0021 b. Components of the chromosomal TFSS exhibited interactions involving: 1) VirD4 and a group of 12 uncharacterized proteins with a common C-terminal domain motif, include XAC2609 whose gene resides within the vir locus; 2) XAC2609 and XAC261 O; 3) Homotropic interactions of VirB11; 4) XAC2622 and VirB9. Analysis of Quorum Sensing/Rpf System components revealed interactions between the principal Rpf proteins which control Xanthomonas quorum sensing: 1) RpfC and RpfF; 2) RpfC and RpfG; 3) RpfF homotropic interactions; 4) RpfC and CmfA, a protein that presents similarity with Cmf (conditioned medium factor) of Dictyostelium discoideum, which contrais quorum sensing in this organism. The protein-protein interactions that we have detected reveal insights into the composition, organization and regulation of these important mechanisms involved in Xanthomonas pathogenicity.

Les travaux de thèse présentés dans ce manuscrit portent sur l'étude de quatre éponges marines issues de la zone Sud-Ouest de l'Océan Indien : Plakortis kenyensis, Theonella swinhoei, Haliclona fascigera et Fascaplysinopsis reticulata. Les travaux entrepris comprenaient l'étude chimique de ces éponges incluant l'extraction, l'isolement et l'identification des métabolites secondaires par différentes techniques chromatographiques (CLMP, CLHP...) et spectroscopiques (UV-visible, HRMS, RMN 1D et 2D...). Douze métabolites secondaires ont été isolés de ces éponges dont six de structures nouvelles, à savoir : l'acide 2,5-époxydocosan-6-én-21-ynoïque (HF1), un acide gras atypique isolé de l'éponge Haliclona fascigera ; la 8-oxo-tryptamine (FR2), la 6,6’-bis-(débromo)- gelliusine F (FR3), la 6-bromo-2’-déméthyl-3’-N-méthyl-1’,8-dihydroaplysinopsine (FR6), la 5,6-dibromo-2’- déméthyl-3’-N-méthyl-1’,8-dihydroaplysinopsine (FR7) et la 5,6-dibromo-3’-déimino-2’-déméthyl-3’-oxo-1’,8- dihydroaplysinopsine (FR8), cinq alcaloïdes indoliques isolés de l'éponge Fascaplysinopsis reticulata. La valorisation des molécules isolées a ensuite été envisagée via l'évaluation de leurs activités biologiques. Parmi les douze molécules isolées, sept ont montré une activité antipaludique, trois une activité inhibitrice du quorum sensing de la bactérie bioluminescente Vibrio harveyi et cinq une activité anti-microfouling par inhibition de l'adhésion et/ou de la croissance de souches microbiennes marines. / The work described in this manuscript concerns four sponges from the South-West Indian Ocean: Plakortis kenyensis, Theonella swinhoei, Haliclona fascigera and Fascaplysinopsis reticulata. The chemical study of the sponges including extraction, isolation and identification of secondary metabolites was undertaken using various chromatographic (MPLC, HPLC ...) and spectroscopic (UV-visible, HRMS, 1D and 2D NMR ...) techniques. Twelve secondary metabolites including six new molecules were isolated from these sponges. The new molecules are: 2,5-époxydocosan-6-en-21-ynoic acid (HF1) an unusual fatty acid isolated from the sponge Haliclona fascigera; 8-oxo-tryptamine (FR2), 6,6'-bis (debromo)-gelliusine F (FR3), 6-bromo-2'-demethyl-3'-N- methyl-1',8-dihydroaplysinopsine (FR6), 5,6-dibromo-2'-demethyl-3'-N-methyl-1',8-dihydroaplysinopsine (FR7) and 5,6-dibromo-3’-deimino-2’-demethyl-3’-oxo-1’,8-dihydroaplysinopsine (FR8), five indole alkaloids isolated from the sponge Fascaplysinopsis reticulata. The biological activities of the isolated molecules were then evaluated. Among the twelve isolated molecules, seven were active against the malaria parasite Plasmodium falciparum, three were identified as inhibitors of the quorum sensing-regulated bioluminescence in Vibrio harveyi and five, showing marine bacterial adhesion and/or growth inhibition, exhibited potential anti- microfouling activity.

O trabalho aqui desenvolvido teve como objeto o estudo estrutural e funcional de várias proteínas do fitopatógeno Xanthomonas axonopodis pv citri (Xac), dentre as quais se destacam as proteínas hipotéticas conservadas YaeQ e SufE, as proteínas RpfC, RpfF e RpfG envolvidas em quorum sensing e proteínas PilZ, FimX e PilB envolvidas na biogênese do pilus tipo IV. Para o desenvolvimento deste trabalho foram utilizadas diferentes técnicas incluindo: clonagem, expressão, purificação, desnaturação térmica, cristalografia, difração de raios-X, RMN, ensaios de 2-híbrido, produção de nocautes, mutação sítio dirigida, Western- e Far- Western, entre outras. Dentre os resultados mais importantes obtidos temos a determinação estrutural das proteínas YaeQ e PilZ pela técnica MAD. Em ambos os casos, as estruturas representaram topologias inéditas. Com base nos dados estruturais, mostramos que YaeQ pertence à família PD-(D/E)XK presente em endonucleases dependentes de magnésio, e a partir de ensaios funcionais obtivemos evidências que sugerem que YaeQ está envolvida em alguma via de reparo de DNA em Xac. A estrutura tridimensional de PilZ revelou uma inesperada variedade estrutural dentro da família PilZ e mostrou de forma clara porque ortólogos não interagem com o segundo mensageiro bacteriano, c-diGMP. A cadeia principal de PilZ foi assinalada por RMN e a estrutura secundária de PilZ em solução é consistente com aquela determinada por cristalografia. Duas proteínas que interagem com PilZ foram identificadas: PilB e FimX. Como PilZ, ambos exercem papéis na biogênese do pilus tipo IV (T4P). Mostramos que PilZ interage especificamente com o domínio EAL de FimX e que resíduos conservados na região do C-terminal de PilZ estão envolvidos na interação com PilB, mas não com FimX. Ensaios de mutação sítio dirigida mostraram que a Y22 de PilZ pode estar envolvida na regulação da interação de PilZ com FimX e com PilB. Apesar de PilZ não interagir com c-diGMP seu parceiro, FimX, interage. PilZ consegue interagir com PilB ao mesmo tempo em que interage com FimX, formando um complexo ternário que é independente da interação de FimX com c-diGMP. Com base em todos estes resultados propusemos possíveis mecanismos de ação de PilZ e FimX no controle da biogênese do T4P. Além dos resultados acima descritos, determinamos a estrutura de SufE e mostramos que esta aumenta a atividade cisteína dessulfarase de seu parceiro, SufS, em torno de 10 vezes, como ocorre com SufE-SufS de E.coli. Clonamos, expressamos, purificamos e fizemos ensaios de cristalização de algumas proteínas envolvidas no controle de quorum sensing em Xac. Tivemos êxito na cristalização do domínio HPT (histidina fosfotransferase) da proteína chave deste sistema, RpfC / The aim of the project was to perform structural and functional studies of different Xanthomonas axonopodis pv citri (Xac) proteins including the hypothetical proteins YaeQ and SufE; RpfC, RpfF and RpfG involved in the quorum sensing and PilZ, FimX and PilB that play roles in type IV pilus (T4P) biogenesis. Several experimental techniques were employed including cloning, expression and purification of recombinant proteins, thermal denaturation, protein crystallography, X-ray diffraction, NMR, two-hybrid assays, Western- and Far-Western Blotting assays, site direct mutagenesis, and the production of Xac knockouts strains. The most important results include the determination of the three-dimensional crystal structures of PilZ and YaeQ using the MAD technique. In both cases, the structures reveled new protein topologies. The comparison of the YaeQ structure with others deposited in public databases revealed that YaeQ proteins represent a new variation within the PD-(D/E)XK magnesium dependent endonucleases superfamily. Functional assays suggest that YaeQ may be envolved in DNA repair in Xac. The PilZ three-dimensional structure revealed an unexpected structural variation within the PilZ domain superfamily and showed why PilZ orthologs are not able to bind the important bacterial second messenger, c-diGMP. We assigned the PilZ main chain by NMR and used this information to demonstrate that the PilZ secondary structure in solution is consistent with the PilZ crystal structure. We identified two proteins that interact with PilZ: PilB and FimX. As with PilZ, both PilB and FimX are involved in T4P biogenesis. PilZ binds specifically to the EAL domain of FimX and the conserved residues located in the PilZ unstructured C-terminal region contribute to binding with PilB but not with FimX. Site direct mutagenesis studies showed that PilZ residue Y22 is necessary for its capability to interact with both PilB and FimX. Although PilZ does not bind c-diGMP, her partner, FimX, does. We present evidence that PilZ can bind simultaneously to FimX and PilB, forming a ternary complex that is independent of c-diGMP. These results allow us to propose possible mechanisms by which PilZ and FimX control T4P biogenesis. Other results obtained during this period include the resolution of the crystal structure of the SufE protein from Xac using the molecular replacement technique. We show that SufE induces a 10-fold increase in the cysteine desulfurase activity of SufS, similar to that observed for the SufE-SufS complex from E. coli. Several proteins involved in quorum sensing and c-di-GMP signaling were cloned, expressed and submitted to crystallization trials. Crystals of the HPT (histidine phophotransferase) domain) of the RpfC sensor histidine kinase were obtained