BackgroundCitrus canker is a disease that has severe economic impact on the citrus industry worldwide. There are three types of canker, called A, B, and C. The three types have different phenotypes and affect different citrus species. The causative agent for type A is Xanthomonas citri subsp. citri, whose genome sequence was made available in 2002. Xanthomonas fuscans subsp. aurantifolii strain B causes canker B and Xanthomonas fuscans subsp. aurantifolii strain C causes canker C.ResultsWe have sequenced the genomes of strains B and C to draft status. We have compared their genomic content to X. citri subsp. citri and to other Xanthomonas genomes, with special emphasis on type III secreted effector repertoires. In addition to pthA, already known to be present in all three citrus canker strains, two additional effector genes, xopE3 and xopAI, are also present in all three strains and are both located on the same putative genomic island. These two effector genes, along with one other effector-like gene in the same region, are thus good candidates for being pathogenicity factors on citrus. Numerous gene content differences also exist between the three cankers strains, which can be correlated with their different virulence and host range. Particular attention was placed on the analysis of genes involved in biofilm formation and quorum sensing, type IV secretion, flagellum synthesis and motility, lipopolysacharide synthesis, and on the gene xacPNP, which codes for a natriuretic protein.ConclusionWe have uncovered numerous commonalities and differences in gene content between the genomes of the pathogenic agents causing citrus canker A, B, and C and other Xanthomonas genomes. Molecular genetics can now be employed to determine the role of these genes in plant-microbe interactions. The gained knowledge will be instrumental for improving citrus canker control.

Plant cell walls mostly comprise polysaccharides and proteins. The composition of monocots’ primary cell walls differs from that of dicots walls with respect to the type of hemicelluloses, the reduction of pectin abundance and the presence of aromatic molecules. Cell wall proteins (CWPs) differ among plant species, and their distribution within functional classes varies according to cell types, organs, developmental stages and/or environmental conditions. In this review, we go deeper into the findings of cell wall proteomics in monocot species and make a comparative analysis of the CWPs identified, considering their predicted functions, the organs analyzed, the plant developmental stage and their possible use as targets for biofuel production. Arabidopsis thaliana CWPs were considered as a reference to allow comparisons among different monocots, i.e., Brachypodium distachyon, Saccharum spp. and Oryza sativa. Altogether, 1159 CWPs have been acknowledged, and specificities and similarities are discussed. In particular, a search for A. thaliana homologs of CWPs identified so far in monocots allows the definition of monocot CWPs characteristics. Finally, the analysis of monocot CWPs appears to be a powerful tool for identifying candidate proteins of interest for tailoring cell walls to increase biomass yield of transformation for second-generation biofuels production.

By characterizing the cell wall proteomes of different sugarcane organs (leaves and stems) at two developmental stages (young vs mature/apical vs basal), it is possible to address unique characteristics in each of them. Four-month-old leaves show a higher proportion of oxido-reductases and proteins related to lipid metabolism (LM), besides a lower proportion of proteins acting on polysaccharides, in comparison to 4-month-old internodes. It is possible to note that sugarcane leaves and young stems have the highest LM rate than all species, which is assumed to be linked to cuticle formation. The data generated enrich the number of cell wall proteins (CWPs) identified in sugarcane, reaching 277. To our knowledge, sugarcane has now the second higher coverage of monocot CWP in plants.Plant biomass is one of the most abundant renewable resources [1] and it has been assumed that plants devote more than 10% of their genome to the biogenesis of cell walls. [2] During plant growth and development, plant cell walls are continuously modified by enzyme action [3] which are important players in the remodeling of cell wall components. The identification of cell wall proteins (CWPs) has been performed in various plant organs mainly in model plants such as Arabidopsis thaliana and Brachypodium distachyon, but also in crops. [4,5] These data could also be used as a source of information to identify possible targets for plant engineering to produce tailored-cell walls more easily amenable to saccharification and production of ethanol of second generation (E2G). [6] In this work, we have established the CWP atlas of leaves and stems of 4-month-old sugarcane plants. DOI: 10.1002/pmic.201700129The aim was to identify genes encoding proteins of interest to produce tailored cell walls allowing more efficient production of E2G from sugarcane residues. Pooling samples from leaves and stems internodes at different developmental stages from sugarcane variety SP80-3280 were used. The samples were named according the classification on the work of Kuijper, 1915 [cited in [7] ] in which growth in length of the internodes and of the leaves are completed at stages 4 and 0 respectively (see Figure 1). Basal internodes (BI) referring to 5-7 internodes, apical internodes (AI) referring to 1-3 internodes, mature leaves (ML) referring to 1-3 leaves, and young leaves (YL) referring to -3, -2, and -1 leaves. Plants were acclimated in a greenhouse at controlled temperature (26°C) with daily irrigation. Internodes and leaves were collected after 4 months of growth and their proteins were extracted.For the extraction of CWPs a nondestructive method was used, based on [8] and adapted by [9] . Three biological replicates were performed. It is important to mention that the infiltration protocol mostly recovers weakly-bound and labile proteins, and it was chosen because of the already proven high efficiency in recovering sugarcane CWPs compared to destructive techniques. [9] Protein identification was performed by MS subsequently and protein digest were f...

Uncovering the molecular mechanisms involved in the responses of crops to drought is crucial to understand and enhance drought tolerance mechanisms. Sugarcane (Saccharum spp.) is an important commercial crop cultivated mainly in tropical and subtropical areas for sucrose and ethanol production. Usually, drought tolerance has been investigated by single omics analysis (e.g. global transcripts identification). Here we combine label-free quantitative proteomics and metabolomics data (GC-TOF-MS), using a network-based approach, to understand how two contrasting commercial varieties of sugarcane, CTC15 (tolerant) and SP90-3414 (susceptible), adjust their leaf metabolism in response to drought. To this aim, we propose the utilization of regularized canonical correlation analysis (rCCA), which is a modification of classical CCA, and explores the linear relationships between two datasets of quantitative variables from the same experimental units, with a threshold set to 0.99. Light curves revealed that after 4 days of drought, the susceptible variety had its photosynthetic capacity already significantly reduced, while the tolerant variety did not show major reduction. Upon 12 days of drought, photosynthesis in the susceptible plants was completely reduced, while the tolerant variety was at a third of its rate under control conditions. Network analysis of proteins and metabolites revealed that different biological process had a stronger impact in each variety (e.g. translation in CTC15, generation of precursor metabolites, response to stress and energy in SP90-3414). Our results provide a reference data set and demonstrate that rCCA can be a powerful tool to infer experimentally metabolite-protein or protein-metabolite associations to understand plant biology.

Metabolic pathways are now considered as intrinsic virulence attributes of pathogenic bacteria and thus represent potential targets for antibacterial strategies. Here we focused on the role of the pentose phosphate pathway (PPP) and its connections with other metabolic pathways in the pathophysiology of Francisella novicida. The involvement of the PPP in the intracellular life cycle of Francisella was first demonstrated by studying PPP inactivating mutants. Indeed, we observed that inactivation of the tktA, rpiA or rpe genes severely impaired intramacrophage multiplication during the first 24 hours. However, time-lapse video microscopy demonstrated that rpiA and rpe mutants were able to resume late intracellular multiplication. To better understand the links between PPP and other metabolic networks in the bacterium, we also performed an extensive proteo-metabolomic analysis of these mutants. We show that the PPP constitutes a major bacterial metabolic hub with multiple connections to glycolysis, the tricarboxylic acid cycle and other pathways, such as fatty acid degradation and sulfur metabolism. Altogether our study highlights how PPP plays a key role in the pathogenesis and growth of Francisella in its intracellular niche.