Regulation of D-xylose metabolism in Caulobacter crescentus by a LacI-type repressor

Xylose Isomerase Depletion Enhances Virulence of Xanthomonas citri subsp. citri in Citrus aurantifolia

Citrus canker, caused by the bacterium Xanthomonas citri (Xcc), is one of the most devastating diseases for the citrus industry. Xylose is a constituent of the cell wall of plants, and the ability of Xcc to use this carbohydrate may play a role in virulence. Xcc has two genes codifying for xylose isomerase (XI), a bifunctional enzyme that interconverts D-xylose into D-xylulose and D-glucose into D-fructose. The aim of this work was to investigate the functional role of the two putative XI ORFs, XAC1776 (xylA1) and XAC4225 (xylA2), in Xcc pathogenicity. XI-coding genes of Xcc were deleted, and the single mutants (XccΔxylA1 or XccΔxylA2) or the double mutant (XccΔxylA1ΔxylA2) remained viable. The deletion of one or both XI genes (xylA1 and/or xylA2) increased the aggressiveness of the mutants, causing disease symptoms. RT-qPCR analysis of wild strain and xylA deletion mutants grown in vivo and in vitro revealed that the highest expression level of hrpX and xylR was observed in vivo for the double mutant. The results indicate that XI depletion increases the expression of the hrp regulatory genes in Xcc. We concluded that the intracellular accumulation of xylose enhances Xcc virulence.

D-Xylose Blocks the Broad Negative Regulation of XylR on Lipid Metabolism and Affects Multiple Physiological Characteristics in Mycobacteria

D-xylose is the most abundant fermentable pentose, which usually represents an architectural component of the bacterial cell wall. However, its regulatory function and the involved signaling pathway in bacteria remain largely unclear. Here, we show that D-xylose can act as a signaling molecule to regulate the lipid metabolism and affect multiple physiological characteristics in mycobacteria. D-xylose directly interacts with XylR and inhibits its DNA-binding ability, thus blocking XylR-mediated repression. The xylose inhibitor, XylR, plays a global regulatory role and affects the expression of 166 mycobacterial genes that are involved in lipid synthesis and metabolism. Furthermore, we show that the xylose-dependent gene regulation of XylR affects the multiple physiological characteristics of Mycobacterium smegmatis, including bacterial size, colony phenotype, biofilm formation, cell aggregation, and antibiotic resistance. Finally, we found that XylR inhibited the survival of Mycobacterium bovis BCG in the host. Our findings provide novel insights into the molecular mechanism of lipid metabolism regulation and its correlation with bacterial physiological phenotypes.

Global Cellular Metabolic Rewiring Adapts Corynebacterium glutamicum to Efficient Nonnatural Xylose Utilization

Xylose, the major component of lignocellulosic biomass, cannot be naturally or efficiently utilized by most microorganisms. Xylose (co)utilization is considered a cornerstone of efficient lignocellulose-based biomanufacturing. We evolved a rapidly xylose-utilizing strain, Cev2-18-5, which showed the highest reported specific growth rate (0.357 h^-1) on xylose among plasmid-free Corynebacterium glutamicum strains. A genetically clear chassis strain, CGS15, was correspondingly reconstructed with an efficient glucose-xylose coutilization performance based on comparative genomic analysis and mutation reconstruction. With the introduction of a succinate-producing plasmid, the resulting strain, CGS15-SA1, can efficiently produce 97.1 g/L of succinate with an average productivity of 8.09 g/L/h by simultaneously utilizing glucose and xylose from corn stalk hydrolysate. We further revealed a novel xylose regulatory mechanism mediated by the endogenous transcription factor IpsA with global regulatory effects on C. glutamicum. A synergistic effect on carbon metabolism and energy supply, motivated by three genomic mutations (P_sod(C131T)-xylAB, P_tuf(Δ21)-araE, and ipsA^C331T), was found to endow C. glutamicum with the efficient xylose utilization and rapid growth phenotype. Overall, this work not only provides promising C. glutamicum chassis strains for a lignocellulosic biorefinery but also enriches the understanding of the xylose regulatory mechanism. IMPORTANCE A novel xylose regulatory mechanism mediated by the transcription factor IpsA was revealed. A synergistic effect on carbon metabolism and energy supply was found to endow C. glutamicum with the efficient xylose utilization and rapid growth phenotype. The new xylose regulatory mechanism enriches the understanding of nonnatural substrate metabolism and encourages exploration new engineering targets for rapid xylose utilization. This work also provides a paradigm to understand and engineer the metabolism of nonnatural renewable substrates for sustainable biomanufacturing.

Melon/cowpea intercropping pattern influenced the N and C soil cycling and the abundance of soil rare bacterial taxa

The high use of pesticides, herbicides, and unsustainable farming practices resulted in losses of soil quality. Sustainable farming practices such as intercropping could be a good alternative to traditional monocrop, especially using legumes such as cowpea (Vigna unguiculata L. Walp). In this study, different melon and cowpea intercropping patterns (melon mixed with cowpea in the same row (MC1); alternating one melon row and one cowpea row (MC2); alternating two melon rows and one cowpea row (MC3)) were assayed to study the intercropping effect on soil bacterial community through 16S rRNA region in a 3-year experiment. The results indicated that intercropping showed high content of total organic carbon, total nitrogen and ammonium, melon yield, and bacterial diversity as well as higher levels of beneficial soil microorganisms such a Pseudomonas, Aeromicrobium, Niastella, or Sphingomonas which can promote plant growth and plant defense against pathogens. Furthermore, intercropping showed a higher rare taxa diversity in two (MC1 and MC2) out of the three intercropping systems. In addition, N-cycling genes such as nirB, nosZ, and amoA were more abundant in MC1 and MC2 whereas the narG predicted gene was far more abundant in the intercropping systems than in the monocrop at the end of the 3-year experiment. This research fills a gap in knowledge about the importance of soil bacteria in an intercropping melon/cowpea pattern, showing the benefits to yield and soil quality with a decrease in N fertilization.

D-Xylose Sensing in Saccharomyces cerevisiae: Insights from D-Glucose Signaling and Native D-Xylose Utilizers

Extension of the substrate range is among one of the metabolic engineering goals for microorganisms used in biotechnological processes because it enables the use of a wide range of raw materials as substrates. One of the most prominent examples is the engineering of baker's yeast Saccharomyces cerevisiae for the utilization of d-xylose, a five-carbon sugar found in high abundance in lignocellulosic biomass and a key substrate to achieve good process economy in chemical production from renewable and non-edible plant feedstocks. Despite many excellent engineering strategies that have allowed recombinant S. cerevisiae to ferment d-xylose to ethanol at high yields, the consumption rate of d-xylose is still significantly lower than that of its preferred sugar d-glucose. In mixed d-glucose/d-xylose cultivations, d-xylose is only utilized after d-glucose depletion, which leads to prolonged process times and added costs. Due to this limitation, the response on d-xylose in the native sugar signaling pathways has emerged as a promising next-level engineering target. Here we review the current status of the knowledge of the response of S. cerevisiae signaling pathways to d-xylose. To do this, we first summarize the response of the native sensing and signaling pathways in S. cerevisiae to d-glucose (the preferred sugar of the yeast). Using the d-glucose case as a point of reference, we then proceed to discuss the known signaling response to d-xylose in S. cerevisiae and current attempts of improving the response by signaling engineering using native targets and synthetic (non-native) regulatory circuits.

Engineering of xylose metabolism in Escherichia coli for the production of valuable compounds

The lignocellulosic sugar d-xylose has recently gained prominence as an inexpensive alternative substrate for the production of value-added compounds using genetically modified organisms. Among the prokaryotes, Escherichia coli has become the de facto host for the development of engineered microbial cell factories. The favored status of E. coli resulted from a century of scientific explorations leading to a deep understanding of its systems. However, there are limited literature reviews that discuss engineered E. coli as a platform for the conversion of d-xylose to any target compounds. Additionally, available critical review articles tend to focus on products rather than the host itself. This review aims to provide relevant and current information about significant advances in the metabolic engineering of d-xylose metabolism in E. coli. This focusses on unconventional and synthetic d-xylose metabolic pathways as several review articles have already discussed the engineering of native d-xylose metabolism. This paper, in particular, is essential to those who are working on engineering of d-xylose metabolism using E. coli as the host.

Role of error-prone DNA polymerases in spontaneous mutagenesis in Caulobacter crescentus

Spontaneous mutations are important players in evolution. Nevertheless, there is a paucity of information about the mutagenic processes operating in most bacterial species. In this work, we implemented two forward mutational markers for studies in Caulobacter crescentus. We confirmed previous results in which A:T → G:C transitions are the most prevalent type of spontaneous base substitutions in this organism, although there is considerable deviation from this trend in one of the loci analyzed. We also investigated the role of dinB and imuC, encoding error-prone DNA polymerases, in spontaneous mutagenesis in this GC-rich organism. Both dinB and imuC mutant strains show comparable mutation rates to the parental strain. Nevertheless, both strains show differences in the base substitution patterns, and the dinB mutant strain shows a striking reduction in the number of spontaneous -1 deletions and an increase in C:G → T:A transitions in both assays.

Biochemical routes for uptake and conversion of xylose by microorganisms

Xylose is a major component of lignocellulose and the second most abundant sugar present in nature. Efficient utilization of xylose is required for the development of economically viable processes to produce biofuels and chemicals from biomass. However, there are still some bottlenecks in the bioconversion of xylose, including the fact that some microorganisms cannot assimilate xylose naturally and that the uptake and metabolism of xylose are inhibited by glucose, which is usually present with xylose in lignocellulose hydrolysate. To overcome these issues, numerous efforts have been made to discover, characterize, and engineer the transporters and enzymes involved in xylose utilization to relieve glucose inhibition and to develop recombinant microorganisms to produce fuels and chemicals from xylose. Here we describe a recent advancement focusing on xylose-utilizing pathways, biosynthesis of chemicals from xylose, and engineering strategies used to improve the conversion efficiency of xylose.

AraR, an L-Arabinose-Responding Transcription Factor, Negatively Regulates Resistance of Mycobacterium smegmatis to Isoniazid

L-Arabinose is an important component of mycobacterial cell wall. L-Arabinose is involved in the synthesis of arabinogalactan, lipoarabinomannan, and other sugar compounds, which suggests that it can modulate cell wall permeability and drug resistance. However, whether L-arabinose affects mycobacterial antibiotic resistance and the underlying regulatory mechanism remains unclear. In this study, we characterized a new transcription factor of Mycobacterium smegmatis, AraR, that responds to L-arabinose and regulates mycobacterial sensitivity to isoniazid (INH). AraR specifically recognizes two conserved 15-bp motifs within the upstream regulatory region of the arabinose (araR) operon. AraR functions as a transcriptional repressor that negatively regulates araR expression. In contrast to the effect of AraR, overexpression of the araR operon contributes to the mycobacterial INH resistance. L-arabinose acts as an effector and derepresses transcriptional inhibition by AraR. The araR-deficient strain is more resistant to INH than the wild-type strain, whereas the araR-overexpressing strain is more sensitive to INH. Addition of L-arabinose to the medium can significantly increase the resistance to INH of the wild-type strain, but not of the araR knockout strain. Therefore, we identified a new L-arabinose-responding transcription factor and revealed its effect on the bacterial antibiotic resistance. These findings can provide new insights in the regulatory mechanisms mediated by sugar molecules and their relationship with drug resistance in mycobacteria.

Uptake of D-xylose and L-arabinose in Haloferax volcanii involves an ABC transporter of the CUT1 subfamily

Haloferax volcanii degrades D-xylose and L-arabinose via an oxidative pathway to α-ketoglutarate as an intermediate. The enzymes of this pathway are encoded by the xac gene cluster (xylose and arabinose catabolism) which also contains genes (xacGHIJK) that encode all components of a putative ABC transporter. The xacGHIJK genes encode one substrate binding protein, two transmembrane domains and two nucleotide binding domains. It is shown here, that xacGHIJK is upregulated by both D-xylose and L-arabinose mediated by the transcriptional regulator XacR, the general regulator of xac genes. Knock-out mutants of xacG and of xacGHIJK resulted in a reduced growth rate on both pentoses; wild type growth could be recovered by complementation in trans. Together, the data indicate that uptake of xylose and arabinose in H. volcanii is mediated by this ABC transporter. Pentose specific ABC transporters, homologous to that of H. volcanii, were identified in other haloarchaea suggesting a similar function in pentose uptake in these archaea. Sequence analyses attribute the haloarchaeal pentose ABC transporter to the CUT1 (carbohydrate uptake transporter 1) subfamily.

Genome-scale fitness profile of Caulobacter crescentus grown in natural freshwater

Bacterial genomes evolve in complex ecosystems and are best understood in this natural context, but replicating such conditions in the lab is challenging. We used transposon sequencing to define the fitness consequences of gene disruption in the bacterium Caulobacter crescentus grown in natural freshwater, compared with axenic growth in common laboratory media. Gene disruptions in amino-acid and nucleotide sugar biosynthesis pathways and in metabolic substrate transport machinery impaired fitness in both lake water and defined minimal medium relative to complex peptone broth. Fitness in lake water was enhanced by insertions in genes required for flagellum biosynthesis and reduced by insertions in genes involved in biosynthesis of the holdfast surface adhesin. We further uncovered numerous hypothetical and uncharacterized genes for which disruption impaired fitness in lake water, defined minimal medium, or both. At the genome scale, the fitness profile of mutants cultivated in lake water was more similar to that in complex peptone broth than in defined minimal medium. Microfiltration of lake water did not significantly affect the terminal cell density or the fitness profile of the transposon mutant pool, suggesting that Caulobacter does not strongly interact with other microbes in this ecosystem on the measured timescale. Fitness of select mutants with defects in cell surface biosynthesis and environmental sensing were significantly more variable across days in lake water than in defined medium, presumably owing to day-to-day heterogeneity in the lake environment. This study reveals genetic interactions between Caulobacter and a natural freshwater environment, and provides a new avenue to study gene function in complex ecosystems.

Control of proline utilization by the Lrp-like regulator PutR in Caulobacter crescentus

Cellular metabolism recently emerged as a central player modulating the bacterial cell cycle. The Alphaproteobacterium Caulobacter crescentus appears as one of the best models to study these connections, but its metabolism is still poorly characterized. Considering that it lives in oligotrophic environments, its capacity to use amino-acids is often critical for its growth. Here, we characterized the C. crescentus PutA bi-functional enzyme and showed that it is required for the utilization of proline as a carbon source. We also found that putA transcription and proline utilization by PutA are strictly dependent on the Lrp-like PutR activator. The activation of putA by PutR needs proline, which most likely acts as an effector molecule for PutR. Surprisingly, we also observed that an over-production of PutR leads to cell elongation in liquid medium containing proline, while it inhibits colony formation even in the absence of proline on solid medium. These cell division and growth defects were equally pronounced in a ΔputA mutant background, indicating that PutR can play other roles beyond the control of proline catabolism. Altogether, these findings suggest that PutR might connect central metabolism with cell cycle processes.

Everyone loves an underdog: metabolic engineering of the xylose oxidative pathway in recombinant microorganisms

The D-xylose oxidative pathway (XOP) has recently been employed in several recombinant microorganisms for growth or for the production of several valuable compounds. The XOP is initiated by D-xylose oxidation to D-xylonolactone, which is then hydrolyzed into D-xylonic acid. D-Xylonic acid is then dehydrated to form 2-keto-3-deoxy-D-xylonic acid, which may be further dehydrated then oxidized into α-ketoglutarate or undergo aldol cleavage to form pyruvate and glycolaldehyde. This review introduces a brief discussion about XOP and its discovery in bacteria and archaea, such as Caulobacter crescentus and Haloferax volcanii. Furthermore, the current advances in the metabolic engineering of recombinant strains employing the XOP are discussed. This includes utilization of XOP for the production of diols, triols, and short-chain organic acids in Escherichia coli, Saccharomyces cerevisiae, and Corynebacterium glutamicum. Improving the D-xylose uptake, growth yields, and product titer through several metabolic engineering techniques bring some of these recombinant strains close to industrial viability. However, more developments are still needed to optimize the XOP pathway in the host strains, particularly in the minimization of by-product formation.

Concomitant Regulation by a LacI-Type Transcriptional Repressor XylR on Genes Involved in Xylan and Xylose Metabolism and the Type III Secretion System in Rice Pathogen Xanthomonas oryzae pv. oryzae

The hypersensitive response and pathogenicity (hrp) genes of Xanthomonas oryzae pv. oryzae, the causal agent of bacterial leaf blight of rice, encode components of the type III secretion system and are essential for virulence. Expression of hrp genes is regulated by two key hrp regulators, HrpG and HrpX; HrpG regulates hrpX and hrpA, and HrpX regulates the other hrp genes on hrpB-hrpF operons. We previously reported the sugar-dependent quantitative regulation of HrpX; the regulator highly accumulates in the presence of xylose, followed by high hrp gene expression. Here, we found that, in a mutant lacking the LacI-type transcriptional regulator XylR, HrpX accumulation and hrp gene expression were high even in the medium without xylose, reaching the similar levels present in the wild type incubated in the xylose-containing medium. XylR also negatively regulated one of two xylose isomerase genes (xylA2 but not xylA1) by binding to the motif sequence in the upstream region of the gene. Xylose isomerase is an essential enzyme in xylose metabolism and interconverts between xylose and xylulose. Our results suggest that, in the presence of xylose, inactivation of XylR leads to greater xylan and xylose utilization and, simultaneously, to higher accumulation of HrpX, followed by higher hrp gene expression in the bacterium.

Metabolic engineering of a xylose pathway for biotechnological production of glycolate in Escherichia coli

BACKGROUND

Glycolate is a valuable chemical with extensive applications in many different fields. The traditional methods to synthesize glycolate are quite expensive and toxic. So, the biotechnological production of glycolate from sustainable feedstocks is of interest for its potential economic and environmental advantages. D-Xylose is the second most abundant sugar in nature and accounts for 18-30% of sugar in lignocellulose. New routes for the conversion of xylose to glycolate were explored.

RESULTS

Overexpression of aceA and ghrA and deletion of aceB in Escherichia coli were examined for glycolate production from xylose, but the conversion was initially ineffective. Then, a new route for glycolate production was established in E. coli by introducing NAD⁺-dependent xylose dehydrogenase (xdh) and xylonolactonase (xylC) from Caulobacter crescentus. The constructed engineered strain Q2562 produced 28.82 ± 0.56 g/L glycolate from xylose with 0.60 ± 0.01 g/L/h productivity and 0.38 ± 0.07 g/g xylose yield. However, 27.18 ± 2.13 g/L acetate was accumulated after fermentation. Deletions of iclR and ackA were used to overcome the acetate excretion. An ackA knockout resulted in about 66% decrease in acetate formation. The final engineered strain Q2742 produced 43.60 ± 1.22 g/L glycolate, with 0.91 ± 0.02 g/L/h productivity and 0.46 ± 0.03 g/g xylose yield.

CONCLUSIONS

A new route for glycolate production from xylose was established, and an engineered strain Q2742 was constructed from this new explored pathway. The engineering strain showed the highest reported productivity of glycolate to date. This research opened up a new prospect for bio-refinery of xylose and an alternative choice for industrial production of glycolate.

Exopolysaccharide production in Caulobacter crescentus: A resource allocation trade-off between protection and proliferation

Complex and interacting selective pressures can produce bacterial communities with a range of phenotypes. One measure of bacterial success is the ability of cells or populations to proliferate while avoiding lytic phage infection. Resistance against bacteriophage infection can occur in the form of a metabolically expensive exopolysaccharide capsule. Here, we show that in Caulobacter crescentus, presence of an exopolysaccharide capsule provides measurable protection against infection from a lytic paracrystalline S-layer bacteriophage (CR30), but at a metabolic cost that reduces success in a phage-free environment. Carbon flux through GDP-mannose 4,6 dehydratase in different catabolic and anabolic pathways appears to mediate this trade-off. Together, our data support a model in which diversity in bacterial communities may be maintained through variable selection on phenotypes utilizing the same metabolic pathway.

Characterization and mutagenesis of two novel iron-sulphur cluster pentonate dehydratases

We describe here the identification and characterization of two novel enzymes belonging to the IlvD/EDD protein family, the D-xylonate dehydratase from Caulobacter crescentus, Cc XyDHT, (EC 4.2.1.82), and the L-arabonate dehydratase from Rhizobium leguminosarum bv. trifolii, Rl ArDHT (EC 4.2.1.25), that produce the corresponding 2-keto-3-deoxy-sugar acids. There is only a very limited amount of characterization data available on pentonate dehydratases, even though the enzymes from these oxidative pathways have potential applications with plant biomass pentose sugars. The two bacterial enzymes share 41 % amino acid sequence identity and were expressed and purified from Escherichia coli as homotetrameric proteins. Both dehydratases were shown to accept pentonate and hexonate sugar acids as their substrates and require Mg(2+) for their activity. Cc XyDHT displayed the highest activity on D-xylonate and D-gluconate, while Rl ArDHT functioned best on D-fuconate, L-arabonate and D-galactonate. The configuration of the OH groups at C2 and C3 position of the sugar acid were shown to be critical, and the C4 configuration also contributed substantially to the substrate recognition. The two enzymes were also shown to contain an iron-sulphur [Fe-S] cluster. Our phylogenetic analysis and mutagenesis studies demonstrated that the three conserved cysteine residues in the aldonic acid dehydratase group of IlvD/EDD family members, those of C60, C128 and C201 in Cc XyDHT, and of C59, C127 and C200 in Rl ArDHT, are needed for coordination of the [Fe-S] cluster. The iron-sulphur cluster was shown to be crucial for the catalytic activity (kcat) but not for the substrate binding (Km) of the two pentonate dehydratases.

Analysis of a taurine-dependent promoter in Sinorhizobium meliloti that offers tight modulation of gene expression

Background

Genetic models have been developed in divergent branches of the class Alphaproteobacteria to help answer a wide spectrum of questions regarding bacterial physiology. For example, Sinorhizobium meliloti serves as a useful representative for investigating rhizobia-plant symbiosis and nitrogen fixation, Caulobacter crescentus for studying cell cycle regulation and organelle biogenesis, and Zymomonas mobilis for assessing the potentials of metabolic engineering and biofuel production. A tightly regulated promoter that enables titratable expression of a cloned gene in these different models is highly desirable, as it can facilitate observation of phenotypes that would otherwise be obfuscated by leaky expression.

Results

We compared the functionality of four promoter regions in S. meliloti (P_araA, P_tauA, P_rhaR, and P_melA) by constructing strains carrying fusions to the uidA reporter in their genomes and measuring beta-glucuronidase activities when they were induced by arabinose, taurine, rhamnose, or melibiose. P_tauA was chosen for further study because it, and, to a lesser extent, P_melA, exhibited characteristics suitable for efficient modulation of gene expression. The levels of expression from P_tauA depended on the concentrations of taurine, in both complex and defined media, in S. meliloti as well as C. crescentus and Z. mobilis. Moreover, our analysis indicated that TauR, TauC, and TauY are each necessary for taurine catabolism and substantiated their designated roles as a transcriptional activator, the permease component of an ABC transporter, and a major subunit of the taurine dehydrogenase, respectively. Finally, we demonstrated that P_tauA can be used to deplete essential cellular factors in S. meliloti, such as the PleC histidine kinase and TatB, a component of the twin-arginine transport machinery.

Conclusions

The P_tauA promoter of S. meliloti can control gene expression with a relatively inexpensive and permeable inducer, taurine, in diverse alpha-proteobacteria. Regulated expression of the same gene in different hosts can be achieved by placing both tauR and P_tauA on appropriate vectors, thus facilitating inspection of conservation of gene function across species.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-014-0295-2) contains supplementary material, which is available to authorized users.

XacR - a novel transcriptional regulator of D-xylose and L-arabinose catabolism in the haloarchaeon Haloferax volcanii

The haloarchaeon Haloferax volcanii degrades D-xylose and L-arabinose via oxidative pathways to α-ketoglutarate. The genes involved in these pathways are clustered and were transcriptionally upregulated by both D-xylose and L-arabinose suggesting a common regulator. Adjacent to the gene cluster, a putative IclR-like transcriptional regulator, HVO_B0040, was identified. It is shown that HVO_B0040, designated xacR, encodes an activator of both D-xylose and L-arabinose catabolism: in ΔxacR cells, transcripts of genes involved in pentose catabolism could not be detected; transcript formation could be recovered by complementation, indicating XacR dependent transcriptional activation. Upstream activation promoter regions and nucleotide sequences that were essential for XacR-mediated activation of pentose-specific genes were identified by in vivo deletion and scanning mutagenesis. Besides its activator function XacR acted as repressor of its own synthesis: xacR deletion resulted in an increase of xacR promoter activity. A palindromic sequence was identified at the operator site of xacR promoter, and mutation of this sequence also resulted in an increase and thus derepression of xacR promoter activity. It is concluded that the palindromic sequence represents the binding site of XacR as repressor. This is the first report of a transcriptional regulator of pentose catabolism in the domain of archaea.

Extracellular gluco-oligosaccharide degradation by Caulobacter crescentus

The oligotrophic bacterium Caulobacter crescentus has the ability to metabolize various organic molecules, including plant structural carbohydrates, as a carbon source. The nature of β-glucosidase (BGL)-mediated gluco-oligosaccharide degradation and nutrient transport across the outer membrane in C. crescentus was investigated. All gluco-oligosaccharides tested (up to celloheptose) supported growth in M2 minimal media but not cellulose or CM-cellulose. The periplasmic and outer membrane fractions showed highest BGL activity, but no significant BGL activity was observed in the cytosol or extracellular medium. Cells grown in cellobiose showed expression of specific BGLs and TonB-dependent receptors (TBDRs). Carbonyl cyanide 3-chlorophenylhydrazone lowered the rate of cell growth in cellobiose but not in glucose, indicating potential cellobiose transport into the cell by a proton motive force-dependent process, such as TBDR-dependent transport, and facilitated diffusion of glucose across the outer membrane via specific porins. These results suggest that C. crescentus acquires carbon from cellulose-derived gluco-oligosaccharides found in the environment by extracellular and periplasmic BGL activity and TBDR-mediated transport. This report on extracellular degradation of gluco-oligosaccharides and methods of nutrient acquisition by C. crescentus supports a broader suite of carbohydrate metabolic capabilities suggested by the C. crescentus genome sequence that until now have not been reported.

Cumate-inducible gene expression system for sphingomonads and other Alphaproteobacteria

Tunable promoters represent a pivotal genetic tool for a wide range of applications. Here we present such a system for sphingomonads, a phylogenetically diverse group of bacteria that have gained much interest for their potential in bioremediation and their use in industry and for which no dedicated inducible gene expression system has been described so far. A strong, constitutive synthetic promoter was first identified through a genetic screen and subsequently combined with the repressor and the operator sites of the Pseudomonas putida F1 cym/cmt system. The resulting promoter, termed PQ5, responds rapidly to the inducer cumate and shows a maximal induction ratio of 2 to 3 orders of magnitude in the different sphingomonads tested. Moreover, it was also functional in other Alphaproteobacteria, such as the model organisms Caulobacter crescentus, Paracoccus denitrificans, and Methylobacterium extorquens. In the noninduced state, expression from PQ5 is low enough to allow gene depletion analysis, as demonstrated with the essential gene phyP of Sphingomonas sp. strain Fr1. A set of PQ5-based plasmids has been constructed allowing fusions to affinity tags or fluorescent proteins.

The xylan utilization system of the plant pathogen Xanthomonas campestris pv campestris controls epiphytic life and reveals common features with oligotrophic bacteria and animal gut symbionts

Xylan is a major structural component of plant cell wall and the second most abundant plant polysaccharide in nature. Here, by combining genomic and functional analyses, we provide a comprehensive picture of xylan utilization by Xanthomonas campestris pv campestris (Xcc) and highlight its role in the adaptation of this epiphytic phytopathogen to the phyllosphere. The xylanolytic activity of Xcc depends on xylan-deconstruction enzymes but also on transporters, including two TonB-dependent outer membrane transporters (TBDTs) which belong to operons necessary for efficient growth in the presence of xylo-oligosaccharides and for optimal survival on plant leaves. Genes of this xylan utilization system are specifically induced by xylo-oligosaccharides and repressed by a LacI-family regulator named XylR. Part of the xylanolytic machinery of Xcc, including TBDT genes, displays a high degree of conservation with the xylose-regulon of the oligotrophic aquatic bacterium Caulobacter crescentus. Moreover, it shares common features, including the presence of TBDTs, with the xylan utilization systems of Bacteroides ovatus and Prevotella bryantii, two gut symbionts. These similarities and our results support an important role for TBDTs and xylan utilization systems for bacterial adaptation in the phyllosphere, oligotrophic environments and animal guts.

Statistical analysis of pentose phosphate pathway genes from eubacteria and eukarya reveals translational selection as a major force in shaping codon usage pattern

Comparative analysis of metabolic pathways among widely diverse species provides an excellent opportunity to extract information about the functional relation of organisms and pentose phosphate pathway exemplifies one such pathway. A comparative codon usage analysis of the pentose phosphate pathway genes of a diverse group of organisms representing different niches and the related factors affecting codon usage with special reference to the major forces influencing codon usage patterns was carried out. It was observed that organism specific codon usage bias percolates into vital metabolic pathway genes irrespective of their near universality. A clear distinction in the codon usage pattern of gram positive and gram negative bacteria, which is a major classification criterion for bacteria, in terms of pentose phosphate pathway was an important observation of this study. The codon utilization scheme in all the organisms indicates the presence of translation selection as a major force in shaping codon usage. Another key observation was the segregation of the H. sapiens genes as a separate cluster by correspondence analysis, which is primarily attributed to the different codon usage pattern in this genus along with its longer gene lengths. We have also analyzed the amino acid distribution comparison of transketolase protein primary structures among all the organisms and found that there is a certain degree of predictability in the composition profile except in A. fumigatus and H. sapiens, where few exceptions are prominent. In A. fumigatus, a human pathogen responsible for invasive aspergillosis, a significantly different codon usage pattern, which finally translated into its amino acid composition model portraying a unique profile in a key pentose phosphate pathway enzyme transketolase was observed.

Structures of the Escherichia coli transcription activator and regulator of diauxie, XylR: an AraC DNA-binding family member with a LacI/GalR ligand-binding domain

Escherichia coli can rapidly switch to the metabolism of l-arabinose and d-xylose in the absence of its preferred carbon source, glucose, in a process called carbon catabolite repression. Transcription of the genes required for l-arabinose and d-xylose consumption is regulated by the sugar-responsive transcription factors, AraC and XylR. E. coli represents a promising candidate for biofuel production through the metabolism of hemicellulose, which is composed of d-xylose and l-arabinose. Understanding the l-arabinose/d-xylose regulatory network is key for such biocatalyst development. Unlike AraC, which is a well-studied protein, little is known about XylR. To gain insight into XylR function, we performed biochemical and structural studies. XylR contains a C-terminal AraC-like domain. However, its N-terminal d-xylose-binding domain contains a periplasmic-binding protein (PBP) fold with structural homology to LacI/GalR transcription regulators. Like LacI/GalR proteins, the XylR PBP domain mediates dimerization. However, unlike LacI/GalR proteins, which dimerize in a parallel, side-to-side manner, XylR PBP dimers are antiparallel. Strikingly, d-xylose binding to this domain results in a helix to strand transition at the dimer interface that reorients both DNA-binding domains, allowing them to bind and loop distant operator sites. Thus, the combined data reveal the ligand-induced activation mechanism of a new family of DNA-binding proteins.

Evidence of a plasmid-encoded oxidative xylose-catabolic pathway in Arthrobacter nicotinovorans pAO1

Due to its high abundance, the D-xylose fraction of lignocellulose provides a promising resource for production of various chemicals. Examples of efficient utilization of d-xylose are nevertheless rare, mainly due to the lack of enzymes with suitable properties for biotechnological applications. The genus Arthrobacter, which occupies an ecological niche rich in lignocellulosic materials and containing species with high resistance and tolerance to environmental factors, is a very suitable candidate for finding D-xylose-degrading enzymes with new properties. In this work, the presence of the pAO1 megaplasmid in cells of Arthrobacter nicotinovorans was directly linked to the ability of this microorganism to ferment D-xylose and to sustain longer log growth. Three pAO1 genes (orf32, orf39, orf40) putatively involved in degradation of xylose were identified and cloned, and the corresponding proteins purified and characterized. ORF40 was shown to be a homotetrameric NADP(+)/NAD(+) sugar dehydrogenase with a strong preference for d-xylose; ORF39 is a monomeric aldehyde dehydrogenase with wide substrate specificity and ORF32 is a constitutive expressed transcription factor putatively involved in control of the entire catabolic pathway. Based on analogies with other pentose degradation pathways, a putative xylose oxidative pathway similar to the Weimberg pathway is postulated.

Metabolic engineering of D-xylose pathway in Clostridium beijerinckii to optimize solvent production from xylose mother liquid

Clostridium beijerinckii is an attractive butanol-producing microbe for its advantage in co-fermenting hexose and pentose sugars. However, this Clostridium strain exhibits undesired efficiency in utilizing D-xylose, one of the major building blocks contained in lignocellulosic materials. Here, we reported a useful metabolic engineering strategy to improve D-xylose consumption by C. beijerinckii. Gene cbei2385, encoding a putative D-xylose repressor XylR, was first disrupted in the C. beijerinckii NCIMB 8052, resulting in a significant increase in D-xylose consumption. A D-xylose proton-symporter (encoded by gene cbei0109) was identified and then overexpressed to further optimize D-xylose utilization, yielding an engineered strain 8052xylR-xylT(ptb) (xylR inactivation plus xylT overexpression driven by ptb promoter). We investigated the strain 8052xylR-xylT(ptb) in fermenting xylose mother liquid, an abundant by-product from industrial-scale xylose preparation from corncob and rich in D-xylose, finally achieving a 35% higher Acetone, Butanol and Ethanol (ABE) solvent titer (16.91 g/L) and a 38% higher yield (0.29 g/g) over those of the wild-type strain. The strategy used in this study enables C. beijerinckii more suitable for butanol production from lignocellulosic materials.

CztR, a LysR-type transcriptional regulator involved in zinc homeostasis and oxidative stress defense in Caulobacter crescentus

Caulobacter crescentus is a free-living alphaproteobacterium that has 11 predicted LysR-type transcriptional regulators (LTTRs). Previously, a C. crescentus mutant strain with a mini-Tn5lacZ transposon inserted into a gene encoding an LTTR was isolated; this mutant was sensitive to cadmium. In this work, a mutant strain with a deletion was obtained, and the role of this LTTR (called CztR here) was evaluated. The transcriptional start site of this gene was determined by primer extension analysis, and its promoter was cloned in front of a lacZ reporter gene. β-galactosidase activity assays, performed with the wild-type and mutant strains, indicated that this gene is 2-fold induced when cells enter stationary phase and that it is negatively autoregulated. Moreover, this regulator is essential for the expression of the divergent cztA gene at stationary phase, in minimal medium, and in response to zinc depletion. This gene encodes a hypothetical protein containing 10 predicted transmembrane segments, and its expression pattern suggests that it encodes a putative zinc transporter. The cztR strain was also shown to be sensitive to superoxide (generated by paraquat) and to hydrogen peroxide but not to tert-butyl hydroperoxide. The expression of katG and ahpC, but not that of the superoxide dismutase genes, was increased in the cztR mutant. A model is proposed to explain how CztR binding to the divergent regulatory regions could activate cztA expression and repress its own transcription.

Identification of a dehydrogenase required for lactose metabolism in Caulobacter crescentus

Caulobacter crescentus, which thrives in freshwater environments with low nutrient levels, serves as a model system for studying bacterial cell cycle regulation and organelle development. We examined its ability to utilize lactose (i) to gain insight into the metabolic capacities of oligotrophic bacteria and (ii) to obtain an additional genetic tool for studying this model organism, aiming to eliminate the basal enzymatic activity that hydrolyzes the chromogenic substrate 5-bromo-4-chloro-3-indolyl-beta-d-galactopyranoside (X-gal). Using a previously isolated transposon mutant, we identified a gene, lacA, that is required for growth on lactose as the sole carbon source and for turning colonies blue in the presence of X-gal. LacA, which contains a glucose-methanol-choline (GMC) oxidoreductase domain, has homology to the flavin subunit of Pectobacterium cypripedii's gluconate dehydrogenase. Sequence comparisons indicated that two genes near lacA, lacB and lacC, encode the other subunits of the membrane-bound dehydrogenase. In addition to lactose, all three lac genes are involved in the catabolism of three other beta-galactosides (lactulose, lactitol, and methyl-beta-d-galactoside) and two glucosides (salicin and trehalose). Dehydrogenase assays confirmed that the lac gene products oxidize lactose, salicin, and trehalose. This enzymatic activity is inducible, and increased lac expression in the presence of lactose and salicin likely contributes to the induction. Expression of lacA also depends on the presence of the lac genes, implying that the dehydrogenase participates in induction. The involvement of a dehydrogenase suggests that degradation of lactose and other sugars in C. crescentus may resemble a proposed pathway in Agrobacterium tumefaciens.

Broad-host-range expression vectors with tightly regulated promoters and their use to examine the influence of TraR and TraM expression on Ti plasmid quorum sensing

Experiments requiring strong repression and precise control of cloned genes can be difficult to conduct because of the relatively high basal level of expression of currently employed promoters. We report the construction of a family of vectors that contain a reengineered lacI(q)-lac promoter-operator complex in which cloned genes are strongly repressed in the absence of inducer. The vectors, all based on the broad-host-range plasmid pBBR1, are mobilizable and stably replicate at moderate copy number in representatives of the alpha- and gammaproteobacteria. Each vector contains a versatile multiple cloning site that includes an NdeI site allowing fusion of the cloned gene to the initiation codon of lacZalpha. In each tested bacterium, a uidA reporter fused to the promoter was not expressed at a detectable level in the absence of induction but was inducible by 10- to 100-fold, depending on the bacterium. The degree of induction was controllable by varying the concentration of inducer. When the vector was tested in Agrobacterium tumefaciens, a cloned copy of the traR gene, the product of which is needed at only a few copies per cell, did not confer activity under noninducing conditions. We used this attribute of very tight and variably regulatable control to assess the relative amounts of TraR required to activate the Ti plasmid conjugative transfer system. We identified levels of induction that gave wild-type transfer frequencies, as well as levels that induced correspondingly lower frequencies of transfer. We also used this system to show that the antiactivator TraM sets the level of intracellular TraR required for tra gene activation.