BackgroundSpecies of the genus Halomonas are salt-tolerant organisms that have a versatile metabolism and can degrade a variety of xenobiotic compounds, utilizing them as their sole carbon source. In this study, we examined the genome of a Halomonas isolate from a hydrocarbon-contaminated site to search for chemosensory genes that might be responsible for the observed chemotactic behavior of this organism as well as for other responses to environmental cues.ResultsUsing genome-wide comparative tools, our isolate was identified as a strain of Halomonas titanicae (strain KHS3), together with two other Halomonas strains with available genomes that had not been previously identified at a species level.The search for the main components of chemosensory pathways resulted in the identification of two clusters of chemosensory genes and a total of twenty-five chemoreceptor genes.One of the gene clusters is very similar to the che cluster from Escherichia coli and, presumably, it is responsible for the chemotactic behavior towards a variety of compounds. This gene cluster is present in 47 out of 56 analyzed Halomonas strains with available genomes.A second che-like cluster includes a gene coding for a diguanylate cyclase with a phosphotransfer and two receiver domains, as well as a gene coding for a chemoreceptor with a longer cytoplasmic domain than the other twenty-four. This seemingly independent pathway resembles the wsp pathway from Pseudomonas aeruginosa although it also presents several differences in gene order and domain composition. This second chemosensory gene cluster is only present in a sub-group within the genus Halomonas. Moreover, remarkably similar gene clusters are also found in some orders of Proteobacteria phylogenetically more distant from the Oceanospirillales, suggesting the occurrence of lateral transfer events.ConclusionsChemosensory pathways were investigated within the genus Halomonas. A canonical chemotaxis pathway, controlled by a variable number of chemoreceptors, is widespread among Halomonas species. A second chemosensory pathway of unique organization that involves some type of c-di-GMP signaling was found to be present only in one branch of the genus, as well as in other proteobacterial lineages.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4655-4) contains supplementary material, which is available to authorized users.

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The draft genome sequence of Halomonas sp. KHS3, isolated from seawater from Mar del Plata harbor, is reported. This strain is able to grow using aromatic compounds as a carbon source and shows strong chemotactic response toward these substrates. Genes involved in motility, chemotaxis, and degradation of aromatic hydrocarbons were identified.

Pyruvate is a central metabolite that connects many metabolic pathways in living organisms. To meet the cellular pyruvate requirements, the enterobacterium Escherichia coli has at least three pyruvate uptake systems—the H+/pyruvate symporter BtsT, and two thus far less well-characterized transporters, YhjX and CstA. BtsT and CstA belong to the putative carbon starvation (CstA) family (transporter classification TC# 2.A.114). We have created an E. coli mutant that cannot grow on pyruvate as the sole carbon source and used it to characterize CstA as a pyruvate transporter. Transport studies in intact cells confirmed that CstA is a highly specific pyruvate transporter with moderate affinity and is energized by a proton gradient. When cells of a reporter strain were cultured in complex medium, cstA expression was maximal only in stationary phase. A DNA affinity-capture assay combined with mass spectrometry and an in-vivo reporter assay identified Fis as a repressor of cstA expression, in addition to the known activator cAMP-CRP. The functional characterization and regulation of this second pyruvate uptake system provides valuable information for understanding the complexity of pyruvate sensing and uptake in E. coli.

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Chemotaxis represents a survival strategy that allows microorganisms to perceive changes in the surrounding environment and actively move toward favorable conditions. An amazingly conserved signaling system (Wuichet & Zhulin, 2010) comprises chemoreceptors or MCPs (for Methyl-accepting Chemotaxis Proteins) that control an associated histidine kinase in response to environmental signals. This kinase in turn phosphorylates a response regulator that alters either the swimming behavior through interaction with the flagellar motors (reviewed in Parkinson et al., 2015), or other ways of bacterial movement (Kaimer & Zusman, 2016) to cause net movement toward attractants or away from repellents.Enteric bacteria, the microorganisms where the chemotaxis system has been extensively studied, possess a single set of chemotaxis genes. In general, microorganisms inhabiting stable niches have simple chemotaxis systems with few chemoreceptors, while environmental bacteria that need to cope with varying conditions have more complex chemotaxis systems and a higher number of chemoreceptors (Lacal et al., 2010). Canonical chemoreceptors that sense chemical signals from the medium possess a periplasmic ligand-binding domain (LBD) flanked by two transmembrane segments. The cytoplasmic portion of the receptor comprises, in many cases, a HAMP domain (signal-transducing module that is present in Histidine kinases, Adenylyl cyclases, MCPs,

Pyruvate is a key metabolite in living cells and has been shown to play a crucial role in the virulence of several bacterial pathogens. The bioluminescent Vibrio campbellii , a severe infectious burden for marine aquaculture, excretes extraordinarily large amounts of pyruvate during growth and rapidly retrieves it by an as-yet unknown mechanism. We have now identified the responsible pyruvate transporter, here named BtsU, and our results show that it is the only pyruvate transporter in V. campbellii . Expression of btsU is tightly regulated by the membrane-integrated LytS-type histidine kinase BtsS, a sensor for extracellular pyruvate, and the LytTR-type response regulator BtsR. Cells lacking either the pyruvate transporter or sensing system show no chemotactic response towards pyruvate, indicating that intracellular pyruvate is required to activate the chemotaxis system. Moreover, pyruvate sensing and uptake were found to be important for the resuscitation of V. campbellii from the viable but nonculturable (VBNC) state and the bacterium’s virulence against brine shrimp larvae. IMPORTANCE Bacterial infections are a serious threat to marine aquaculture, one of the fastest growing food sectors on earth. Therefore, it is extremely important to learn more about the pathogens responsible, one of which is Vibrio campbellii . This study sheds light on the importance of pyruvate sensing and uptake for V. campbellii , and reveals that the bacterium possesses only one pyruvate transporter, which is activated by a pyruvate-responsive histidine kinase/response regulator system. Without the ability to sense or take up pyruvate, the virulence of V. campbellii towards gnotobiotic brine shrimp larvae is strongly reduced.

SummaryChemoreceptors transmit signals from the environment to the flagellar motors via a histidine kinase that controls the phosphorylation level of the effector protein CheY. The cytoplasmic domain of chemoreceptors is strongly conserved and consists of a long alpha-helical hairpin that forms, in the dimer, a coiledcoil four-helix bundle. Changes in this domain during evolution are characterized by the presence of sevenresidue insertions/deletions located symmetrically with respect to the hairpin turn, suggesting that specific interactions between the helices that form the hairpin are required for function. We assessed the impact of seven-residue deletions on the signalling ability and higher-order organization of the serine chemoreceptor from Escherichia coli. Our results indicate that symmetry alterations between the two branches of the cytoplasmic hairpin seriously compromise chemoreceptor function. Shorter functional versions of Tsr with symmetrical deletions form mixed trimers of dimers when coexpressed with Tar, the aspartate receptor of E. coli. However, Tar function in those cells is impaired, suggesting that the length difference between receptors introduces nonfunctional distortions into the chemoreceptor cluster. This observation is reinforced by the analysis of coexpression of Tar with chemoreceptors from Rhodobacter sphaeroides that naturally belong to a shorter-length class.