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author:("Becker, ante")
1.  Challenges and perspectives in combinatorial assembly of novel exopolysaccharide biosynthesis pathways 
Because of their rheological properties various microbial polysaccharides are applied as thickeners and viscosifiers both in food and non-food industries. A broad variety of microorganisms secrete structurally diverse exopolysaccharides (EPS) that contribute to their surface attachment, protection against abiotic or biotic stress factors, and nutrient gathering. Theoretically, a massive number of EPS structures are possible through variations in monosaccharide sequences, condensation linkages and non-sugar decorations. Given the already-high diversity of EPS structures, taken together with the principal of combinatorial biosynthetic pathways, microbial polysaccharides are an attractive class of macromolecules with which to generate novel structures via synthetic biology approaches. However, previous manipulations primarily focused on increasing polysaccharide yield, with structural modifications restricted to removal of side chains or non-sugar decorations. This article outlines the biosynthetic pathways of the bacterial heteroexopolysaccharides xanthan and succinoglycan, which are used as thickening and stabilizing agents in food and non-food industries. Challenges and perspectives of combining synthetic biology approaches with directed evolution to overcome obstacles in assembly of novel EPS biosynthesis pathways are discussed.
PMCID: PMC4496566  PMID: 26217319
polysaccharide; synthetic biology; glycosyltransferase; synthase-dependent pathway; ABC transporter-dependent pathway; Wzx/Wzy-dependent pathway
2.  Riboregulation in plant-associated α-proteobacteria 
RNA Biology  2014;11(5):550-562.
The symbiotic α-rhizobia Sinorhizobium meliloti, Bradyrhizobium japonicum, Rhizobium etli and the related plant pathogen Agrobacterium tumefaciens are important model organisms for studying plant-microbe interactions. These metabolically versatile soil bacteria are characterized by complex lifestyles and large genomes. Here we summarize the recent knowledge on their small non-coding RNAs (sRNAs) including conservation, function, and interaction of the sRNAs with the RNA chaperone Hfq. In each of these organisms, an inventory of hundreds of cis- and trans-encoded sRNAs with regulatory potential was uncovered by high-throughput approaches and used for the construction of 39 sRNA family models. Genome-wide analyses of hfq mutants and co-immunoprecipitation with tagged Hfq revealed a major impact of the RNA chaperone on the physiology of plant-associated α-proteobacteria including symbiosis and virulence. Highly conserved members of the SmelC411 family are the AbcR sRNAs, which predominantly regulate ABC transport systems. AbcR1 of A. tumefaciens controls the uptake of the plant-generated signaling molecule GABA and is a central regulator of nutrient uptake systems. It has similar functions in S. meliloti and the human pathogen Brucella abortus. As RNA degradation is an important process in RNA-based gene regulation, a short overview on ribonucleases in plant-associated α-proteobacteria concludes this review.
PMCID: PMC4152362  PMID: 25003187
RNA-binding protein; RNA-seq; Rhizobiales; antisense RNA; non-coding RNA; ribolysis; riboregulation; sRNA; α-proteobacteria
3.  Genome-wide profiling of Hfq-binding RNAs uncovers extensive post-transcriptional rewiring of major stress response and symbiotic regulons in Sinorhizobium meliloti 
RNA Biology  2014;11(5):563-579.
The RNA chaperone Hfq is a global post-transcriptional regulator in bacteria. Here, we used RNAseq to analyze RNA populations from the legume symbiont Sinorhizobium meliloti that were co-immunoprecipitated (CoIP-RNA) with a FLAG-tagged Hfq in five growth/stress conditions. Hfq-bound transcripts (1315) were largely identified in stressed bacteria and derived from small RNAs (sRNAs), both trans-encoded (6.4%) and antisense (asRNAs; 6.3%), and mRNAs (86%). Pull-down with Hfq recovered a small proportion of annotated S. meliloti sRNAs (14% of trans-sRNAs and 2% of asRNAs) suggesting a discrete impact of this protein in sRNA pathways. Nonetheless, Hfq selectively stabilized CoIP-enriched sRNAs, anticipating that these interactions are functionally significant. Transcription of 26 Hfq-bound sRNAs was predicted to occur from promoters recognized by the major stress σ factors σE2 or σH1/2. Recovery rates of sRNAs in each of the CoIP–RNA libraries suggest a large impact of Hfq-assisted riboregulation in S. meliloti osmoadaptation. Hfq directly targeted 18% of the predicted S. meliloti mRNAs, which encode functionally diverse proteins involved in transport and metabolism, σE2-dependent stress responses, quorum sensing, flagella biosynthesis, ribosome, and membrane assembly or symbiotic nitrogen fixation. Canonical targeting of the 5′ regions of two of the ABC transporter mRNAs by the homologous Hfq-binding AbcR1 and AbcR2 sRNAs leading to inhibition of protein synthesis was confirmed in vivo. We therefore provide a comprehensive resource for the systems-level deciphering of hitherto unexplored S. meliloti stress and symbiotic post-transcriptional regulons and the identification of Hfq-dependent sRNA–mRNA regulatory pairs.
PMCID: PMC4152363  PMID: 24786641
RNA-binding protein; nitrogen-fixation; riboregulation; sRNA; α-proteobacteria
4.  A Stress-Induced Small RNA Modulates Alpha-Rhizobial Cell Cycle Progression 
PLoS Genetics  2015;11(4):e1005153.
Mechanisms adjusting replication initiation and cell cycle progression in response to environmental conditions are crucial for microbial survival. Functional characterization of the trans-encoded small non-coding RNA (trans-sRNA) EcpR1 in the plant-symbiotic alpha-proteobacterium Sinorhizobium meliloti revealed a role of this class of riboregulators in modulation of cell cycle regulation. EcpR1 is broadly conserved in at least five families of the Rhizobiales and is predicted to form a stable structure with two defined stem-loop domains. In S. meliloti, this trans-sRNA is encoded downstream of the divK-pleD operon. ecpR1 belongs to the stringent response regulon, and its expression was induced by various stress factors and in stationary phase. Induced EcpR1 overproduction led to cell elongation and increased DNA content, while deletion of ecpR1 resulted in reduced competitiveness. Computationally predicted EcpR1 targets were enriched with cell cycle-related mRNAs. Post-transcriptional repression of the cell cycle key regulatory genes gcrA and dnaA mediated by mRNA base-pairing with the strongly conserved loop 1 of EcpR1 was experimentally confirmed by two-plasmid differential gene expression assays and compensatory changes in sRNA and mRNA. Evidence is presented for EcpR1 promoting RNase E-dependent degradation of the dnaA mRNA. We propose that EcpR1 contributes to modulation of cell cycle regulation under detrimental conditions.
Author Summary
Microorganisms frequently encounter adverse conditions unfavorable for cell proliferation. They have evolved diverse mechanisms, including transcriptional control and targeted protein degradation, to adjust cell cycle progression in response to environmental cues. Non-coding RNAs are widespread regulators of various cellular processes in all domains of life. In prokaryotes, trans-encoded small non-coding RNAs (trans-sRNAs) contribute to a rapid cellular response to changing environments, but so far have not been directly related to cell cycle regulation. Here, we report the first example of a trans-sRNA (EcpR1) with two experimentally confirmed targets in the core of cell cycle regulation and demonstrate that in the plant-symbiotic alpha-proteobacterium Sinorhizobium meliloti the regulatory mechanism involves base-pairing of this sRNA with the dnaA and gcrA mRNAs. Most trans-sRNAs are restricted to closely related species, but the stress-induced EcpR1 is broadly conserved in the order of Rhizobiales suggesting an evolutionary advantage conferred by ecpR1. It broadens the functional diversity of prokaryotic sRNAs and adds a new regulatory level to the mechanisms that contribute to interlinking stress responses with the cell cycle machinery.
PMCID: PMC4414408  PMID: 25923724
5.  RNase E Affects the Expression of the Acyl-Homoserine Lactone Synthase Gene sinI in Sinorhizobium meliloti 
Journal of Bacteriology  2014;196(7):1435-1447.
Quorum sensing of Sinorhizobium meliloti relies on N-acyl-homoserine lactones (AHLs) as autoinducers. AHL production increases at high population density, and this depends on the AHL synthase SinI and two transcriptional regulators, SinR and ExpR. Our study demonstrates that ectopic expression of the gene rne, coding for RNase E, an endoribonuclease that is probably essential for growth, prevents the accumulation of AHLs at detectable levels. The ectopic rne expression led to a higher level of rne mRNA and a lower level of sinI mRNA independently of the presence of ExpR, the AHL receptor, and AHLs. In line with this, IPTG (isopropyl-β-d-thiogalactopyranoside)-induced overexpression of rne resulted in a shorter half-life of sinI mRNA and a strong reduction of AHL accumulation. Moreover, using translational sinI-egfp fusions, we found that sinI expression is specifically decreased upon induced overexpression of rne, independently of the presence of the global posttranscriptional regulator Hfq. The 28-nucleotide 5′ untranslated region (UTR) of sinI mRNA was sufficient for this effect. Random amplification of 5′ cDNA ends (5′-RACE) analyses revealed a potential RNase E cleavage site at position +24 between the Shine-Dalgarno site and the translation start site. We postulate therefore that RNase E-dependent degradation of sinI mRNA from the 5′ end is one of the steps mediating a high turnover of sinI mRNA, which allows the Sin quorum-sensing system to respond rapidly to changes in transcriptional control of AHL production.
PMCID: PMC3993346  PMID: 24488310
6.  The DivJ, CbrA and PleC system controls DivK phosphorylation and symbiosis in Sinorhizobium meliloti 
Molecular microbiology  2013;90(1):54-71.
Sinorhizobium meliloti is a soil bacterium that invades the root nodules it induces on Medicago sativa, whereupon it undergoes an alteration of its cell cycle and differentiates into nitrogen-fixing, elongated and polyploid bacteroid with higher membrane permeability. In Caulobacter crescentus, a related alphaproteobacterium, the principal cell cycle regulator, CtrA, is inhibited by the phosphorylated response regulator DivK. The phosphorylation of DivK depends on the histidine kinase DivJ, while PleC is the principal phosphatase for DivK. Despite the importance of the DivJ in C. crescentus, the mechanistic role of this kinase has never been elucidated in other Alphaproteobacteria.
We show here that the histidine kinases DivJ together with CbrA and PleC participate in a complex phosphorylation system of the essential response regulator DivK in S. meliloti. In particular, DivJ and CbrA are involved in DivK phosphorylation and in turn CtrA inactivation, thereby controlling correct cell cycle progression and the integrity of the cell envelope. In contrast, the essential PleC presumably acts as a phosphatase of DivK. Interestingly, we found that a DivJ mutant is able to elicit nodules and enter plant cells, but fails to establish an effective symbiosis suggesting that proper envelope and/or low CtrA levels are required for symbiosis.
PMCID: PMC3793127  PMID: 23909720
7.  Temporal Expression Program of Quorum Sensing-Based Transcription Regulation in Sinorhizobium meliloti 
Journal of Bacteriology  2013;195(14):3224-3236.
The Sin quorum sensing (QS) system of S. meliloti activates exopolysaccharide and represses flagellum production. The system consists of an N-acyl-homoserine lactone (AHL) synthase, SinI, and at least two LuxR-type regulators, SinR and ExpR. SinR appears to be independent of AHLs for its control of sinI expression, while ExpR is almost completely dependent upon AHLs. In this study, we confirmed 7 previously detected ExpR-DNA binding sites and used the consensus sequence to identify another 26 sites, some of which regulate genes previously not known to be members of the ExpR/AHL regulon. The activities of promoters dependent upon ExpR/AHL were titrated against AHL levels, with varied outcomes in AHL sensitivity. The data suggest a type of temporal expression program whereby the activity of each promoter is subject to a specific range of AHL concentrations. For example, genes responsible for exopolysaccharide production are activated at lower concentrations of AHLs than those required for the repression of genes controlling flagellum production. Several features of ExpR-regulated promoters appear to determine their response to AHLs. The location of the ExpR-binding site with respect to the relevant transcription start within each promoter region determines whether ExpR/AHL activates or represses promoter activity. Furthermore, the strength of the response is dependent upon the concentration of AHLs. We propose that this differential sensitivity to AHLs provides a bacterial colony with a transcription control program that is dynamic and precise.
PMCID: PMC3697639  PMID: 23687265
8.  Small RNA sX13: A Multifaceted Regulator of Virulence in the Plant Pathogen Xanthomonas 
PLoS Pathogens  2013;9(9):e1003626.
Small noncoding RNAs (sRNAs) are ubiquitous posttranscriptional regulators of gene expression. Using the model plant-pathogenic bacterium Xanthomonas campestris pv. vesicatoria (Xcv), we investigated the highly expressed and conserved sRNA sX13 in detail. Deletion of sX13 impinged on Xcv virulence and the expression of genes encoding components and substrates of the Hrp type III secretion (T3S) system. qRT-PCR analyses revealed that sX13 promotes mRNA accumulation of HrpX, a key regulator of the T3S system, whereas the mRNA level of the master regulator HrpG was unaffected. Complementation studies suggest that sX13 acts upstream of HrpG. Microarray analyses identified 63 sX13-regulated genes, which are involved in signal transduction, motility, transcriptional and posttranscriptional regulation and virulence. Structure analyses of in vitro transcribed sX13 revealed a structure with three stable stems and three apical C-rich loops. A computational search for putative regulatory motifs revealed that sX13-repressed mRNAs predominantly harbor G-rich motifs in proximity of translation start sites. Mutation of sX13 loops differentially affected Xcv virulence and the mRNA abundance of putative targets. Using a GFP-based reporter system, we demonstrated that sX13-mediated repression of protein synthesis requires both the C-rich motifs in sX13 and G-rich motifs in potential target mRNAs. Although the RNA-binding protein Hfq was dispensable for sX13 activity, the hfq mRNA and Hfq::GFP abundance were negatively regulated by sX13. In addition, we found that G-rich motifs in sX13-repressed mRNAs can serve as translational enhancers and are located at the ribosome-binding site in 5% of all protein-coding Xcv genes. Our study revealed that sX13 represents a novel class of virulence regulators and provides insights into sRNA-mediated modulation of adaptive processes in the plant pathogen Xanthomonas.
Author Summary
Since the discovery of the first regulatory RNA in 1981, hundreds of small RNAs (sRNAs) have been identified in bacteria. Although sRNA-mediated control of virulence was demonstrated for numerous animal- and human-pathogenic bacteria, sRNAs and their functions in plant-pathogenic bacteria have been enigmatic. We discovered that the sRNA sX13 is a novel virulence regulator of Xanthomonas campestris pv. vesicatoria (Xcv), which causes bacterial spot disease on pepper and tomato. sX13 contributes to the Xcv-plant interaction by promoting the synthesis of an essential pathogenicity factor of Xcv, i. e., the type III secretion system. Thus, in addition to transcriptional regulation, sRNA-mediated posttranscriptional regulation contributes to virulence of plant-pathogenic xanthomonads. To repress target mRNAs carrying G-rich motifs, sX13 employs C-rich loops. Hence, sX13 exhibits striking structural similarity to sRNAs in distantly related human pathogens, e. g., Staphylococcus aureus and Helicobacter pylori, suggesting that structure-driven target regulation via C-rich motifs represents a conserved feature of sRNA-mediated posttranscriptional regulation. Furthermore, sX13 is the first sRNA shown to control the mRNA level of hfq, which encodes a conserved RNA-binding protein required for sRNA activity and virulence in many enteric bacteria.
PMCID: PMC3771888  PMID: 24068933
9.  Linking Plant Nutritional Status to Plant-Microbe Interactions 
PLoS ONE  2013;8(7):e68555.
Plants have developed a wide-range of adaptations to overcome nutrient limitation, including changes to the quantity and composition of carbon-containing compounds released by roots. Root-associated bacteria are largely influenced by these compounds which can be perceived as signals or substrates. Here, we evaluate the effect of root exudates collected from maize plants grown under nitrogen (N), phosphate (P), iron (Fe) and potassium (K) deficiencies on the transcriptome of the plant growth promoting rhizobacterium (PGPR) Bacillus amyloliquefaciens FZB42. The largest shifts in gene expression patterns were observed in cells exposed to exudates from N-, followed by P-deficient plants. Exudates from N-deprived maize triggered a general stress response in FZB42 in the exponential growth phase, which was evidenced by the suppression of numerous genes involved in protein synthesis. Exudates from P-deficient plants induced bacterial genes involved in chemotaxis and motility whilst exudates released by Fe and K deficient plants did not cause dramatic changes in the bacterial transcriptome during exponential growth phase. Global transcriptional changes in bacteria elicited by nutrient deficient maize exudates were significantly correlated with concentrations of the amino acids aspartate, valine and glutamate in root exudates suggesting that transcriptional profiling of FZB42 associated with metabolomics of N, P, Fe and K-deficient maize root exudates is a powerful approach to better understand plant-microbe interactions under conditions of nutritional stress.
PMCID: PMC3713015  PMID: 23874669
10.  Global mapping of transcription start sites and promoter motifs in the symbiotic α-proteobacterium Sinorhizobium meliloti 1021 
BMC Genomics  2013;14:156.
Sinorhizobium meliloti is a soil-dwelling α-proteobacterium that possesses a large, tripartite genome and engages in a nitrogen fixing symbiosis with its plant hosts. Although much is known about this important model organism, global characterization of genetic regulatory circuits has been hampered by a lack of information about transcription and promoters.
Using an RNAseq approach and RNA populations representing 16 different growth and stress conditions, we comprehensively mapped S. meliloti transcription start sites (TSS). Our work identified 17,001 TSS that we grouped into six categories based on the genomic context of their transcripts: mRNA (4,430 TSS assigned to 2,657 protein-coding genes), leaderless mRNAs (171), putative mRNAs (425), internal sense transcripts (7,650), antisense RNA (3,720), and trans-encoded sRNAs (605). We used this TSS information to identify transcription factor binding sites and putative promoter sequences recognized by seven of the 15 known S. meliloti σ factors σ70, σ54, σH1, σH2, σE1, σE2, and σE9). Altogether, we predicted 2,770 new promoter sequences, including 1,302 located upstream of protein coding genes and 722 located upstream of antisense RNA or trans-encoded sRNA genes. To validate promoter predictions for targets of the general stress response σ factor, RpoE2 (σE2), we identified rpoE2-dependent genes using microarrays and confirmed TSS for a subset of these by 5′ RACE mapping.
By identifying TSS and promoters on a global scale, our work provides a firm foundation for the continued study of S. meliloti gene expression with relation to gene organization, σ factors and other transcription factors, and regulatory RNAs.
PMCID: PMC3616915  PMID: 23497287
Transcription; RNAseq; Transcription start site; Promoter; Sigma factor; Sinorhizobium meliloti; mRNA; sRNA; Antisense RNA
11.  Genome Sequence of Sinorhizobium meliloti Rm41 
Genome Announcements  2013;1(1):e00013-12.
Sinorhizobium meliloti Rm41 nodulates alfalfa plants, forming indeterminate type nodules. It is characterized by a strain-specific K-antigen able to replace exopolysaccharides in promotion of nodule invasion. We present the Rm41 genome, composed of one chromosome, the chromid pSymB, the megaplasmid pSymA, and the nonsymbiotic plasmid pRme41a.
PMCID: PMC3556828  PMID: 23405285
12.  Quantitative Proteomic Analysis of the Hfq-Regulon in Sinorhizobium meliloti 2011 
PLoS ONE  2012;7(10):e48494.
Riboregulation stands for RNA-based control of gene expression. In bacteria, small non-coding RNAs (sRNAs) are a major class of riboregulatory elements, most of which act at the post-transcriptional level by base-pairing target mRNA genes. The RNA chaperone Hfq facilitates antisense interactions between target mRNAs and regulatory sRNAs, thus influencing mRNA stability and/or translation rate. In the α-proteobacterium Sinorhizobium meliloti strain 2011, the identification and detection of multiple sRNAs genes and the broadly pleitropic phenotype associated to the absence of a functional Hfq protein both support the existence of riboregulatory circuits controlling gene expression to ensure the fitness of this bacterium in both free living and symbiotic conditions. In order to identify target mRNAs subject to Hfq-dependent riboregulation, we have compared the proteome of an hfq mutant and the wild type S. meliloti by quantitative proteomics following protein labelling with 15N. Among 2139 univocally identified proteins, a total of 195 proteins showed a differential abundance between the Hfq mutant and the wild type strain; 65 proteins accumulated ≥2-fold whereas 130 were downregulated (≤0.5-fold) in the absence of Hfq. This profound proteomic impact implies a major role for Hfq on regulation of diverse physiological processes in S. meliloti, from transport of small molecules to homeostasis of iron and nitrogen. Changes in the cellular levels of proteins involved in transport of nucleotides, peptides and amino acids, and in iron homeostasis, were confirmed with phenotypic assays. These results represent the first quantitative proteomic analysis in S. meliloti. The comparative analysis of the hfq mutant proteome allowed identification of novel strongly Hfq-regulated genes in S. meliloti.
PMCID: PMC3484140  PMID: 23119037
13.  Genome Sequence of the Soybean Symbiont Sinorhizobium fredii HH103 
Journal of Bacteriology  2012;194(6):1617-1618.
Sinorhizobium fredii HH103 is a fast-growing rhizobial strain that is able to nodulate legumes that develop determinate nodules, e.g., soybean, and legumes that form nodules of the indeterminate type. Here we present the genome of HH103, which consists of one chromosome and five plasmids with a total size of 7.22 Mb.
PMCID: PMC3294874  PMID: 22374952
14.  Transcriptomic profiling of Bacillus amyloliquefaciens FZB42 in response to maize root exudates 
BMC Microbiology  2012;12:116.
Plant root exudates have been shown to play an important role in mediating interactions between plant growth-promoting rhizobacteria (PGPR) and their host plants. Most investigations were performed on Gram-negative rhizobacteria, while much less is known about Gram-positive rhizobacteria. To elucidate early responses of PGPR to root exudates, we investigated changes in the transcriptome of a Gram-positive PGPR to plant root exudates.
Bacillus amyloliquefaciens FZB42 is a well-studied Gram-positive PGPR. To obtain a comprehensive overview of FZB42 gene expression in response to maize root exudates, microarray experiments were performed. A total of 302 genes representing 8.2% of the FZB42 transcriptome showed significantly altered expression levels in the presence of root exudates. The majority of the genes (261) was up-regulated after incubation of FZB42 with root exudates, whereas only 41 genes were down-regulated. Several groups of the genes which were strongly induced by the root exudates are involved in metabolic pathways relating to nutrient utilization, bacterial chemotaxis and motility, and non-ribosomal synthesis of antimicrobial peptides and polyketides.
Here we present a transcriptome analysis of the root-colonizing bacterium Bacillus amyloliquefaciens FZB42 in response to maize root exudates. The 302 genes identified as being differentially transcribed are proposed to be involved in interactions of Gram-positive bacteria with plants.
PMCID: PMC3438084  PMID: 22720735
15.  Environmental Factors Affecting the Expression of pilAB as Well as the Proteome and Transcriptome of the Grass Endophyte Azoarcus sp. Strain BH72 
PLoS ONE  2012;7(1):e30421.
Bacterial communication is involved in regulation of cellular mechanisms such as metabolic processes, microbe-host interactions or biofilm formation. In the nitrogen-fixing model endophyte of grasses Azoarcus sp. strain BH72, known cell-cell signaling systems have not been identified; however, the pilA gene encoding the structural protein of type IV pili that are essential for plant colonization appears to be regulated in a population density-dependent manner.
Methodology/Principal Findings
Our data suggest that pilAB expression is affected by population density, independent of autoinducers typical for Gram-negative bacteria, likely depending on unknown secreted molecule(s) that can be produced by different bacterial species. We used transcriptomic and proteomic approaches to identify target genes and proteins differentially regulated in conditioned supernatants in comparison to standard growth conditions. Around 8% of the 3992 protein-coding genes of Azoarcus sp. and 18% of the detected proteins were differentially regulated. Regulatory proteins and transcription factors among the regulated proteins indicated a complex hierarchy. Differentially regulated genes and proteins were involved in processes such as type IV pili formation and regulation, metal and nutrient transport, energy metabolism, and unknown functions mediated by hypothetical proteins. Four of the newly discovered target genes were further analyzed and in general they showed regulation patterns similar to pilAB. The expression of one of them was shown to be induced in plant roots.
This study is the first global approach to initiate characterization of cell density-dependent gene regulation mediated by soluble molecule(s) in the model endophyte Azoarcus sp. strain BH72. Our data suggest that the putative signaling molecule(s) are also produced by other Proteobacteria and might thus be used for interspecies communication. This study provides the foundation for the development of robust reporter systems for Azoarcus sp. to analyze mechanisms and molecules involved in the population-dependent gene expression in this endophyte in future.
PMCID: PMC3262810  PMID: 22276194
16.  Conservation and Occurrence of Trans-Encoded sRNAs in the Rhizobiales 
Genes  2011;2(4):925-956.
Post-transcriptional regulation by trans-encoded sRNAs, for example via base-pairing with target mRNAs, is a common feature in bacteria and influences various cell processes, e.g., response to stress factors. Several studies based on computational and RNA-seq approaches identified approximately 180 trans-encoded sRNAs in Sinorhizobium meliloti. The initial point of this report is a set of 52 trans-encoded sRNAs derived from the former studies. Sequence homology combined with structural conservation analyses were applied to elucidate the occurrence and distribution of conserved trans-encoded sRNAs in the order of Rhizobiales. This approach resulted in 39 RNA family models (RFMs) which showed various taxonomic distribution patterns. Whereas the majority of RFMs was restricted to Sinorhizobium species or the Rhizobiaceae, members of a few RFMs were more widely distributed in the Rhizobiales. Access to this data is provided via the RhizoGATE portal [1,2].
PMCID: PMC3927594  PMID: 24710299
trans-encoded sRNAs; comparative analyses; Rhizobiales
17.  Insights into the Extracytoplasmic Stress Response of Xanthomonas campestris pv. campestris: Role and Regulation of σE-Dependent Activity ▿ ‡  
Journal of Bacteriology  2010;193(1):246-264.
Xanthomonas campestris pv. campestris is an epiphytic bacterium that can become a vascular pathogen responsible for black rot disease of crucifers. To adapt gene expression in response to ever-changing habitats, phytopathogenic bacteria have evolved signal transduction regulatory pathways, such as extracytoplasmic function (ECF) σ factors. The alternative sigma factor σE, encoded by rpoE, is crucial for envelope stress response and plays a role in the pathogenicity of many bacterial species. Here, we combine different approaches to investigate the role and mechanism of σE-dependent activation in X. campestris pv. campestris. We show that the rpoE gene is organized as a single transcription unit with the anti-σ gene rseA and the protease gene mucD and that rpoE transcription is autoregulated. rseA and mucD transcription is also controlled by a highly conserved σE-dependent promoter within the σE gene sequence. The σE-mediated stress response is required for stationary-phase survival, resistance to cadmium, and adaptation to membrane-perturbing stresses (elevated temperature and ethanol). Using microarray technology, we started to define the σE regulon of X. campestris pv. campestris. These genes encode proteins belonging to different classes, including periplasmic or membrane proteins, biosynthetic enzymes, classical heat shock proteins, and the heat stress σ factor σH. The consensus sequence for the predicted σE-regulated promoter elements is GGAACTN15-17GTCNNA. Determination of the rpoH transcription start site revealed that rpoH was directly regulated by σE under both normal and heat stress conditions. Finally, σE activity is regulated by the putative regulated intramembrane proteolysis (RIP) proteases RseP and DegS, as previously described in many other bacteria. However, our data suggest that RseP and DegS are not only dedicated to RseA cleavage and that the proteolytic cascade of RseA could involve other proteases.
PMCID: PMC3019944  PMID: 20971899
18.  Virulence Evolution of the Human Pathogen Neisseria meningitidis by Recombination in the Core and Accessory Genome 
PLoS ONE  2011;6(4):e18441.
Neisseria meningitidis is a naturally transformable, facultative pathogen colonizing the human nasopharynx. Here, we analyze on a genome-wide level the impact of recombination on gene-complement diversity and virulence evolution in N. meningitidis. We combined comparative genome hybridization using microarrays (mCGH) and multilocus sequence typing (MLST) of 29 meningococcal isolates with computational comparison of a subset of seven meningococcal genome sequences.
Principal Findings
We found that lateral gene transfer of minimal mobile elements as well as prophages are major forces shaping meningococcal population structure. Extensive gene content comparison revealed novel associations of virulence with genetic elements besides the recently discovered meningococcal disease associated (MDA) island. In particular, we identified an association of virulence with a recently described canonical genomic island termed IHT-E and a differential distribution of genes encoding RTX toxin- and two-partner secretion systems among hyperinvasive and non-hyperinvasive lineages. By computationally screening also the core genome for signs of recombination, we provided evidence that about 40% of the meningococcal core genes are affected by recombination primarily within metabolic genes as well as genes involved in DNA replication and repair. By comparison with the results of previous mCGH studies, our data indicated that genetic structuring as revealed by mCGH is stable over time and highly similar for isolates from different geographic origins.
Recombination comprising lateral transfer of entire genes as well as homologous intragenic recombination has a profound impact on meningococcal population structure and genome composition. Our data support the hypothesis that meningococcal virulence is polygenic in nature and that differences in metabolism might contribute to virulence.
PMCID: PMC3082526  PMID: 21541312
19.  Comparative Genome Biology of a Serogroup B Carriage and Disease Strain Supports a Polygenic Nature of Meningococcal Virulence▿ †  
Journal of Bacteriology  2010;192(20):5363-5377.
Neisseria meningitidis serogroup B strains are responsible for most meningococcal cases in the industrialized countries, and strains belonging to the clonal complex ST-41/44 are among the most prevalent serogroup B strains in carriage and disease. Here, we report the first genome and transcriptome comparison of a serogroup B carriage strain from the clonal complex ST-41/44 to the serogroup B disease strain MC58 from the clonal complex ST-32. Both genomes are highly colinear, with only three major genome rearrangements that are associated with the integration of mobile genetic elements. They further differ in about 10% of their gene content, with the highest variability in gene presence as well as gene sequence found for proteins involved in host cell interactions, including Opc, NadA, TonB-dependent receptors, RTX toxin, and two-partner secretion system proteins. Whereas housekeeping genes coding for metabolic functions were highly conserved, there were considerable differences in their expression pattern upon adhesion to human nasopharyngeal cells between both strains, including differences in energy metabolism and stress response. In line with these genomic and transcriptomic differences, both strains also showed marked differences in their in vitro infectivity and in serum resistance. Taken together, these data support the concept of a polygenic nature of meningococcal virulence comprising differences in the repertoire of adhesins as well as in the regulation of metabolic genes and suggest a prominent role for immune selection and genetic drift in shaping the meningococcal genome.
PMCID: PMC2950490  PMID: 20709895
20.  A Normalized Tree Index for identification of correlated clinical parameters in microarray experiments 
BioData Mining  2011;4:2.
Measurements on gene level are widely used to gain new insights in complex diseases e.g. cancer. A promising approach to understand basic biological mechanisms is to combine gene expression profiles and classical clinical parameters. However, the computation of a correlation coefficient between high-dimensional data and such parameters is not covered by traditional statistical methods.
We propose a novel index, the Normalized Tree Index (NTI), to compute a correlation coefficient between the clustering result of high-dimensional microarray data and nominal clinical parameters. The NTI detects correlations between hierarchically clustered microarray data and nominal clinical parameters (labels) and gives a measurement of significance in terms of an empiric p-value of the identified correlations. Therefore, the microarray data is clustered by hierarchical agglomerative clustering using standard settings. In a second step, the computed cluster tree is evaluated. For each label, a NTI is computed measuring the correlation between that label and the clustered microarray data.
The NTI successfully identifies correlated clinical parameters at different levels of significance when applied on two real-world microarray breast cancer data sets. Some of the identified highly correlated labels confirm the actual state of knowledge whereas others help to identify new risk factors and provide a good basis to formulate new hypothesis.
The NTI is a valuable tool in the domain of biomedical data analysis. It allows the identification of correlations between high-dimensional data and nominal labels, while at the same time a p-value measures the level of significance of the detected correlations.
PMCID: PMC3035591  PMID: 21247420
21.  A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti 
BMC Genomics  2010;11:245.
Small untranslated RNAs (sRNAs) are widespread regulators of gene expression in bacteria. This study reports on a comprehensive screen for sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti applying deep sequencing of cDNAs and microarray hybridizations.
A total of 1,125 sRNA candidates that were classified as trans-encoded sRNAs (173), cis-encoded antisense sRNAs (117), mRNA leader transcripts (379), and sense sRNAs overlapping coding regions (456) were identified in a size range of 50 to 348 nucleotides. Among these were transcripts corresponding to 82 previously reported sRNA candidates. Enrichment for RNAs with primary 5'-ends prior to sequencing of cDNAs suggested transcriptional start sites corresponding to 466 predicted sRNA regions. The consensus σ70 promoter motif CTTGAC-N17-CTATAT was found upstream of 101 sRNA candidates. Expression patterns derived from microarray hybridizations provided further information on conditions of expression of a number of sRNA candidates. Furthermore, GenBank, EMBL, DDBJ, PDB, and Rfam databases were searched for homologs of the sRNA candidates identified in this study. Searching Rfam family models with over 1,000 sRNA candidates, re-discovered only those sequences from S. meliloti already known and stored in Rfam, whereas BLAST searches suggested a number of homologs in related alpha-proteobacteria.
The screening data suggests that in S. meliloti about 3% of the genes encode trans-encoded sRNAs and about 2% antisense transcripts. Thus, this first comprehensive screen for sRNAs applying deep sequencing in an alpha-proteobacterium shows that sRNAs also occur in high number in this group of bacteria.
PMCID: PMC2873474  PMID: 20398411
22.  A portal for rhizobial genomes: RhizoGATE integrates a S. meliloti genome annotation update with postgenome data 
Journal of biotechnology  2008;140(1-2):45-50.
Sinorhizobium meliloti is a symbiotic soil bacterium of the alphaproteobacterial subdivision. Like other rhizobia, S. meliloti induces nitrogen-fixing root nodules on leguminous plants. This is an ecologically and economically important interaction, because plants engaged in symbiosis with rhizobia can grow without exogenous nitrogen fertilizers. The S. meliloti-Medicago truncatula (barrel medic) association is an important symbiosis model. The S. meliloti genome was published in 2001, and the Medicago truncatula genome currently is being sequenced. Many new resources and data have been made available since the original S. meliloti genome annotation and an update was needed. In June 2008, we submitted our annotation update to the EMBL and NCBI databases. Here we describe this new annotation and a new web-based portal RhizoGATE. About 1000 annotation updates were made; these included assigning functions to 313 putative proteins, assigning EC numbers to 431 proteins, and identifying 86 new putative genes. RhizoGATE incorporates the new annotion with the S. meliloti GenDB project, a platform that allows annotation updates in real time. Locations of transposon insertions, plasmid integrations, and array probe sequences are available in the GenDB project. RhizoGATE employs the EMMA platform for management and analysis of transcriptome data and the IGetDB data warehouse to integrate a variety of heterogeneous external data sources.
PMCID: PMC2656595  PMID: 19103235
Rhizobiales; α-proteobacteria; symbiotic nitrogen fixation; Medicago; symbiosis
23.  Competitive and Cooperative Effects in Quorum-Sensing-Regulated Galactoglucan Biosynthesis in Sinorhizobium meliloti▿  
Journal of Bacteriology  2008;190(15):5308-5317.
The symbiotic nitrogen-fixing bacterium Sinorhizobium meliloti possesses the Sin quorum-sensing system based on N-acyl homoserine lactones (AHLs) as signal molecules. The Sin system consists of SinI, the AHL synthase, and SinR, the LuxR-type regulator. This system regulates the expression of a multitude of S. meliloti genes through ExpR, another LuxR-type regulator. Analysis of the activity of the sinI promoter showed that the expression of sinI is dependent on sinR and enhanced by a combination of expR and Sin AHLs. The characterization of the ExpR binding site upstream of sinI and the identification of binding sites upstream of the galactoglucan biosynthesis genes wgaA (expA1) and wgeA (expE1) allowed the definition of a consensus sequence for these binding sites. Based on this consensus, two additional ExpR binding sites in the promoter regions of exoI and exsH, two genes related to the production of succinoglycan, were found. The specific binding of ExpR to the wgaA and wgeA promoters was enhanced in the presence of oxo-C14-HL. Positive regulation of the galactoglucan biosynthesis genes by ExpR was shown to be dependent on WggR (ExpG) and influenced by MucR, both of which are previously characterized regulators of these genes. Based on these results, a reworked model of the Sin-ExpR quorum-sensing regulation scheme of galactoglucan production in S. meliloti is suggested.
PMCID: PMC2493264  PMID: 18515420
24.  Prediction of Sinorhizobium meliloti sRNA genes and experimental detection in strain 2011 
BMC Genomics  2008;9:416.
Small non-coding RNAs (sRNAs) have emerged as ubiquitous regulatory elements in bacteria and other life domains. However, few sRNAs have been identified outside several well-studied species of gamma-proteobacteria and thus relatively little is known about the role of RNA-mediated regulation in most other bacterial genera. Here we have conducted a computational prediction of putative sRNA genes in intergenic regions (IgRs) of the symbiotic α-proteobacterium S. meliloti 1021 and experimentally confirmed the expression of dozens of these candidate loci in the closely related strain S. meliloti 2011.
Our first sRNA candidate compilation was based mainly on the output of the sRNAPredictHT algorithm. A thorough manual sequence analysis of the curated list rendered an initial set of 18 IgRs of interest, from which 14 candidates were detected in strain 2011 by Northern blot and/or microarray analysis. Interestingly, the intracellular transcript levels varied in response to various stress conditions. We developed an alternative computational method to more sensitively predict sRNA-encoding genes and score these predicted genes based on several features to allow identification of the strongest candidates. With this novel strategy, we predicted 60 chromosomal independent transcriptional units that, according to our annotation, represent strong candidates for sRNA-encoding genes, including most of the sRNAs experimentally verified in this work and in two other contemporary studies. Additionally, we predicted numerous candidate sRNA genes encoded in megaplasmids pSymA and pSymB. A significant proportion of the chromosomal- and megaplasmid-borne putative sRNA genes were validated by microarray analysis in strain 2011.
Our data extend the number of experimentally detected S. meliloti sRNAs and significantly expand the list of putative sRNA-encoding IgRs in this and closely related α-proteobacteria. In addition, we have developed a computational method that proved useful to predict sRNA-encoding genes in S. meliloti. We anticipate that this predictive approach can be flexibly implemented in many other bacterial species.
PMCID: PMC2573895  PMID: 18793445
25.  Fine-Tuning of Galactoglucan Biosynthesis in Sinorhizobium meliloti by Differential WggR (ExpG)-, PhoB-, and MucR-Dependent Regulation of Two Promoters ▿  
Journal of Bacteriology  2008;190(10):3456-3466.
Depending on the phosphate concentration encountered in the environment Sinorhizobium meliloti 2011 synthesizes two different exopolysaccharides (EPS). Galactoglucan (EPS II) is produced under phosphate starvation but also in the presence of extra copies of the transcriptional regulator WggR (ExpG) or as a consequence of a mutation in mucR. The galactoglucan biosynthesis gene cluster contains the operons wga (expA), wge (expE), wgd (expD), and wggR (expG). Two promoters, differentially controlled by WggR, PhoB, and MucR, were identified upstream of each of these operons. The proximal promoters of the wga, wge, and wgd transcription units were constitutively active when separated from the upstream regulatory sequences. Promoter activity studies and the positions of predicted PhoB and WggR binding sites suggested that the proximal promoters are cooperatively induced by PhoB and WggR. MucR was shown to strongly inhibit the distal promoters and bound to the DNA in the vicinity of the distal transcription start sites. An additional inhibitory effect on the distal promoter of the structural galactoglucan biosynthesis genes was identified as a new feature of WggR in a mucR mutant. A regulatory model of the fine-tuning of galactoglucan production is proposed.
PMCID: PMC2394980  PMID: 18344362

Results 1-25 (38)