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Publications (119)
Rotation of the bacterial flagellum, the first identified biological rotary machine, is driven by its stator units. Knowledge gained about the function of stator units has increasingly led to studies of rotary complexes in different cellular pathways. Here, we report that a tetrameric PilZ family protein, FlgX, is a structural component underneath...
Few aerobic hyperthermophilic microorganisms degrade polysaccharides. Here, we describe the genome-enabled enrichment and optical tweezer-based isolation of an aerobic polysaccharide-degrading hyperthermophile, Fervidibacter sacchari, previously ascribed to candidate phylum Fervidibacteria. F. sacchari uses polysaccharides and monosaccharides for g...
Few aerobic hyperthermophiles degrade polysaccharides. Here, we describe the genome-enabled enrichment and optical tweezer-based isolation of an aerobic polysaccharide-degrading hyperthermophile, Fervidibacter sacchari, which was originally ascribed to candidate phylum Fervidibacteria. F. sacchari uses polysaccharides and monosaccharides as sole ca...
Species of the phylum Actinobacteria have long time been thought mostly non-motile and non-flagellated, in spite of their extraordinary diversity in morphology, physiology, and ecology. It remains unclear how very few actinobacterial species acquired their flagellar genes and the role of flagellar motility in the evolution of different lineages wit...
Campylobacter jejuni is a food-borne zoonotic pathogen of worldwide concern and the leading cause of bacterial diarrheal disease. In contrast to other enteric pathogens, C. jejuni has strict growth and nutritional requirements but lacks many virulence factors that have evolved for pathogenesis or interactions with the host. It is unclear how this b...
The evolution of macromolecular complex is a fundamental biological question, which is related to the origin of life and also guides our practice in synthetic biology. The chemosensory system is one of the complex structures that evolved very early in bacteria and displays enormous diversity and complexity in terms of composition and array structur...
Adaptation to various stresses during infection is important for Salmonella Typhimurium virulence, while the fitness determinants under infection-relevant stress conditions remain unknown. Here, we simulated conditions Salmonella encountered within the host or in the environment by 15 individual stresses as well as two model cell lines (epithelium...
Microbes rely on signal transduction systems to sense and respond to environmental changes for survival and reproduction. It is generally known that niche adaptation plays an important role in shaping the signaling repertoire. However, the evolution of bacterial signaling capacity lacks systematic studies with a temporal direction. In particular, i...
Microbes rely on signal transduction systems to sense and respond to environmental changes for survival and reproduction. It is generally known that niche adaptation plays an important role in shaping the signaling repertoire. However, the evolution of bacterial signaling capacity lacks systematic studies with a temporal direction. Particularly, it...
Cobalamin (vitamin B12) is an essential micronutrient required by both prokaryotes and eukaryotes. Nevertheless, with high genetic and metabolic cost, de novo cobalamin biosynthesis is exclusive to a subset of prokaryotic taxa. Many Cyanobacterial and Archaeal taxa have been implicated in de novo cobalamin biosynthesis in epi- and mesopelagic ocean...
The bacterial flagellum is beneficial in most cases but it can become a burden when the energy source is low because it is very costly to assemble and energize for motility. Recent electron cryo-tomography and real-time fluorescence microscopy studies suggest that bacteria can remove their flagella under starvation in a programmed way.
The class Thermoleophilia is one of the deep-rooting lineages within the Actinobacteria phylum and metagenomic investigation of microbial diversity suggested that species associated with the class Thermoleophilia are abundant in hot spring and soil samples. However, very few species of this class have been cultivated and characterized. Our understa...
Campylobacter jejuni is the leading cause of foodborne gastrointestinal illness worldwide, and chemotaxis plays an important role in its host colonization and pathogenesis. Although many studies on chemotaxis have focused on the physical organization and signaling mechanism of the system's protein complex, much less is known about the transcription...
Recent metagenomic surveys of microbial community suggested that species associated with the class Acidimicrobiia are abundant in diverse aquatic environments such as acidic mine water, waste water sludge, freshwater, or marine habitats, but very few species have been cultivated and characterized. The current taxonomic framework of Acidimicrobiia i...
Campylobacter jejuni is one of the leading infectious causes of food-borne illness around the world. Its ability to persistently colonize the intestinal tract of a broad range of hosts, including food-producing animals, is central to its epidemiology since most infections are due to the consumption of contaminated food products. Using a highly satu...
Amino acid utilization by C. jejuni 81–176 determined by exometabolome analysis.
The uptake of amino acids by C. jejuni 81–176 was examined by measuring their concentrations in the culture supernatants within 24 h of cultivation relative to their original concentration prior to bacterial inoculation, which was considered to be 100%. Shown are the m...
In vivo fitness of C. jejuni insertion mutants determined by INSeq analysis.
Relative abundance of C. jejuni insertion mutants in the inoculum and the mouse cecum samples after infection for 4 (A), 7 (B) and 21 (C) days. In (A) and (B), each point represents the average abundance of read numbers of a single gene obtained from 13 or 5 mice, respecti...
Role of amino acid biosynthesis of C. jejuni 81–176 in mouse colonization.
Illustrated is the impact of amino acid biosynthesis pathways in C. jejuni mouse intestinal colonization as determined by INSeq analysis. Numbers indicate the log2 value of fold change (intestine/inoculum) in the number of insertions in the indicated genes and are derived fr...
Role of methionine and S-adenosyl methionine (SAM) biosynthesis in C. jejuni 81–176 in vivo growth.
Illustrated is the impact of methionine and SAM biosynthesis in C. jejuni mouse intestinal colonization as determined by INSeq analysis. Numbers indicate the log2 value of fold change (intestine/inoculum) in the number of insertions in the indicated...
Impact of the non-oxidative pentose phosphate pathway (PPP) on the growth of C. jejuni 81–176.
Shown is the impact of the inactivation of genes encoding components of the PPP pathway in C. jejuni mouse intestinal colonization as determined by INSeq analyses. Numbers indicate the log2 value of fold change (intestine/inoculum) in the number of insert...
Core metabolic reactions of C. jejuni 81–176 that generate carbon dioxide.
Selected metabolic reactions in C. jejuni that release carbon dioxide (CO2). Numbers indicate the log2 value of fold change (intestine/inoculum) in the number of insertions in the indicated genes and are derived from the raw data in S3 Table. Values below -6.2 indicate mutat...
INSeq raw data for each gene in mouse colonization experiments, which were normalized by median nomarlization method.
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Summary of potassium channel and transporters in Epsilon-proteobacteria.
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Contribution of a C. jejuni motility-associated gene cluster to mouse colonization.
(A)Blue and red bars indicate the normalized read number of each insertion site within the different ORFs in the input and output pool, respectively. Motility assays (B) and growth curves (see S12 Table) (C) for wild-type C. jejuni 81–176 and the ΔCJJ81176_0479, ΔCJ...
Impact of the purine and pyrimidine biosynthesis pathways on the in vivo growth of C. jejuni 81–176.
Shown is the impact of the inactivation of genes encoding components of the purine and pyrimidine biosynthesis pathways in C. jejuni mouse intestinal colonization as determined by INSeq analyses. Numbers indicate the log2 value of fold change (intes...
Analysis of potential polar effects of transposon insertions.
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Strains and plasmids used in this study.
(XLSX)
Raw data for Figs 6E, 7E, S2B, S7C and S10.
(XLSX)
Growth properties of serine-biosynthesis defective C. jejuni mutants.
Wild type C. jejuni 81–176 (WT) and the indicated isogenic mutant strains (serA: D-3-phosphoglycerate dehydrogenase; sdaA: L-serine ammonia-lyase/dehydratase) were grown in defined medium (DAAM) in the presence or absence of serine as indicated. Lactate or glutamate are provided...
13C-incorporation and isotopologue profiles of protein-derived amino acids in C. jejuni 81–176 after incubation with [5-13C1]-Glu in DMEM medium.
Black columns on the left y axis represent percentage of 13C-excess (mol %) into the respective protein-derived amino acids. The colored columns on the right y axis depict the percentages of labeled isoto...
Role of the “acetate switch” in mouse colonization.
Six mice were inoculated with an equal number of wild-type C. jejuni 81–176 and the ΔackA isogenic mutant strain via oral gavage. Competitive indices (CI) were calculated as the ratio of the CFU of the ΔackA mutant over wild type recovered from the ceca of infected mice (see S14 Table).
(TIF)
List of genes that show similar mutant phenotype according to the Venn diagram depicted in Fig 1B and 1C.
(XLSX)
Summary of INSeq data for Tlp and chemotaxis proteins in C. jejuni 81–176.
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Raw data for Figs 2, 5inset, 6C, 6D, S1, S12 and S13.
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Raw data for Figs 7D, S4 and S14.
(XLSX)
Labeling of polar metabolites in C. jejuni 81–176 upon cultivation with [3-13C1]Ser.
Shown are the 13C-incorporation (13C-excess) and the relative isotopologue distributions into polar metabolites isolated from the cytoplasm of C. jejuni after incubation with [3-13C1]Ser. Illustrated are the means ± SD of 6 measurements with the colored boxes indic...
Amino acid uptake ability of C. jejuni 81–176.
(A) Scheme presenting the predicted amino acid uptake capacity of C. jejuni 81–176 according to the INSeq analysis. Viable mutants with transposon insertions in the indicated amino acid biosynthesis pathways have been identified in the screen suggesting the import of respective amino acids. No transpos...
Colony forming units of commensal bacteria in mice feces before and after antibiotic treatment.
Shown is the intestinal bacterial load after antibiotic treatment of animals immediately prior to infection with C. jejuni. Collected feces samples from each mouse were dissolved and diluted serially with PBS buffer, then plated on blood agar in duplicat...
Log2 (output/input) ratio distribution of all insertions during mouse colonization.
Histogram depicting the number of genes (y axis) that exhibited the indicated log2 [fold change (output/input)] change (x axis) in the numbers of transposon insertions recovered from infected mice relative to the number of transposon insertions in the original inocu...
Amino acid composition of all predicted proteins encoded by C. jejuni 81–176.
The frequency of all amino acids in all predicted proteins are shown and branched-chain amino acids are highlighted in orange. Calculations were carried out using BacMap (http://wishart.biology.ualberta.ca/BacMap/cgi/getGraphs.cgi?accession=NC_008787&ref=index_2.html).
(T...
Schematic overview of the 13C-flux into protein-derived amino acids after catabolism of [5-13C1]-Glu in C. jejuni 81–176.
The positions of the 13C-label of the amino acid isotopologues are indicated by the colored dots. Due to the stereoisomerism of the TCA-cycle intermediates succinate and fumarate, it is not possible to distinguish between the C1...
INSeq raw data for each C. jejuni gene after growth under different in-vitro growth condition.
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INSeq raw data for each gene in mouse colonization experiments.
(XLSX)
Growth-promoting substrates utilized by Campylobacter jejuni during colonization of gastrointestinal tract.
(DOCX)
Composition of a modified defined DMEM medium for Campylobacter jejuni 81–176 used in the indicated studies.
(XLSX)
The order Bifidobacteriales comprises a diverse variety of species found in the gastrointestinal tract of humans and other animals, some of which are opportunistic pathogens, whereas a number of others exhibit health-promoting effects. However, currently very few biochemical or molecular characteristics are known which are specific for the order Bi...
Unlabelled:
Motility is essential for the pathogenesis of many bacterial species. Most bacteria move using flagella, which are multiprotein filaments that rotate propelled by a cell wall-anchored motor using chemical energy. Although some components of the flagellar apparatus are common to many bacterial species, recent studies have shown signific...
E-cadherin downregulation in cancer cells is associated with epithelial-to-mesenchymal transition (EMT) and metastatic prowess, but the underlying mechanisms are incompletely characterized. In this study, we probed E-cadherin expression at the plasma membrane as a functional assay to identify genes involved in E-cadherin downregulation. The assay w...
Salmonella Typhimurium has evolved a complex functional interface with its host cell largely determined by two type III secretion systems (T3SS), which through the delivery of bacterial effector proteins modulate a variety of cellular processes. We show here that Salmonella Typhimurium infection of epithelial cells results in a profound transcripti...
Campylobacter jejuni is a major cause of food-borne disease in industrialized countries. Carbohydrate utilization by C. jejuni is severely restricted, and knowledge about which substrates fuel C. jejuni infection and growth is limited. Some amino acids have been shown to serve as carbon sources both in vitro and in vivo. In the present study we inv...
Nucleotide sequence comparison of the L-serine dehydratase sdaA genes in indifferent C. jejuni isolates. The nucleotide sequences of sdaA open reading frames from different C. jejuni strains were compared using ClustalW (www.ebi.ac.uk/Tools/msa/clustalW2). The sources for the DNA sequences are as follows: CG8486 (Cj8486_1666c; NZ_AASY01000001.2), A...
Nucleotide sequence comparison of the serine transporter sdaC genes in different C. jejuni isolates. The published sequences of the sdaC genes from several C. jejuni isolates were compared using ClustalW (www.ebi.ac.uk/Tools/msa/clustalW2). The sources for the nucleotide sequences were obtained from GenBank (NCBI) and have following accession numbe...
Growth of C. jejuni 81-176 and its isogenic sdaA and sdaC mutants. Growth characteristics of the C. jejuni 81-176 wild-type strain, its isogenic sdaC and sdaA mutants as well as a complemented sdaA mutant in DMEM and DMEM supplemented with 20 mM serine, glutamate or proline. The maximal optical densities (OD600) of liquid cultures from indicated C....
Competitive index of mice co-infection with C. jejuni 81-176 and its sdaA, peb1A or putP mutants. The competitive index, CI = (mutantoutput/wild-typeoutput)/(mutantinoculum/wild-typeinoculum), was calculated for each mouse infected with C. jejuni 81-176 wild-type strain and its indicated mutant. The output numbers representing the CFUs of wild-type...
L-serine dehydratase activity in cell extracts of C. jejuni isolates. The mean serine dehydratase activities with standard deviations are shown for measurements repeated four (a) and three (b) times in triplicates. The statistical significance in the differences of SdaA activity between C. jejuni 81-176 and C. jejuni 33251 or RM1221 was calculated...
Comparison of the putA/putP gene cluster in Campylobacter and Enterobacteria. The schematic comparison of the putAputP gene locus and its flanking regions of several Campylobacter and Enterobacter strains was derived from the comparative genome database xBASE2 (Chaudhuri RR et al. (2008) Nucleic Acids Res., D543-6) in particular CampyDB (www.xbase....
Proteobacteria with homologues to the L-serine dehydratase SdaA of C. jejuni 81-176. The table shows the homology between the SdaA protein of C. jejuni 81-176 and the SdaA proteins in other proteobacteria with their given accession numbers. The percent of amino acids identical and similar (conserved amino acid exchanges) between the serine ammonia-...
Strains and plasmids used in this study.
(DOC)
In vitro growth competition experiments of C. jejuni 81-176 and its mutants. Shown are the co-cultivation experiments of C. jejuni 81-176 with its peb1A, putP and sdaA mutants, respectively. Equal amounts of wild-type and a mutant strain were incubated in nutrient rich BHI medium over night and the CFUs of each strain were determined after 20 hours...
Proteobacteria with homologues to the proline dehydrogenase/delta 1-pyrroline-5-carboxylate dehydrogenase PutA of C. jejuni 81-176. The table shows the homology between the PutA protein of C. jejuni 81-176 and the PutA proteins in other proteobacteria with their given accession numbers. The percent of amino acids identical and similar (conserved am...
Amino acid sequence comparison of SdaA proteins from different C. jejuni strains. ClustaW (www.ebi.ac.uk/Tools/msa/clustalW2) was used for the alignment of the SdaA amino acid sequences from various C. jejuni isolates. The accession numbers were as follows: CF93-6 (CJJCF936_1718; ZP_01067690), 84-25 (CJJ8425_1708; ZP_01099834), NCTC 11168 (Cj1624c;...
Comparison of SdaC serine transporter
protein sequences in various C. jejuni isolates. ClustaW (www.ebi.ac.uk/Tools/msa/clustalW2) was used for the alignment of the SdaC amino acid sequences from listed C. jejuni isolates. The protein sequence accession numbers for the SdaC serine transporters of the different C. jejuni strains were as follows: RM1...
Proteobacteria with homologues to the serine transporter SdaC of C. jejuni 81-176. The table shows the homology between the SdaC protein of C. jejuni 81-176 and the SdaC proteins in other proteobacteria. The order represents the grade of homology according to the score calculated by the BlastP algorithm (http://blast.ncbi.nlm.nih.gov/Blast.cgi). C....
Proteobacteria with homologues to the proline transporter PutP of C. jejuni 81-176. The table illustrates the homology between the PutP protein of C. jejuni 81-176 and the PutP proteins in other proteobacteria. The accession numbers of the PutP proteins from indicated bacteria are listed. The order represents the grade of homology according to the...
Primers used in this study.
(DOC)
Spectral counts of C. jejuni proteins detected by LC-MS/MS.
(XLS)
C. jejuni proteins whose levels exhibit significant changes between the 2 h and 20 h samples.
(XLS)
C. jejuni proteins detected in in-vitro grown or obtained from infected cells 2 hs after infection.
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Spectral counts of C. jejuni proteins detected by LC-MS/MS after exposure to infection medium.
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C. jejuni proteins detected 20 hs after infection or after incubation under oxygen -limiting conditions.
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C. jejuni proteins whose levels exhibit significant changes between 20 h after infection and after incubation under low oxygen conditions.
(XLS)
Author Summary
Campylobacter jejuni is one of the most common causes of food-borne illness in the United States and a major cause of diarrheal diseases in developing countries. This pathogen can invade intestinal epithelial cells, which is very important for its ability to cause disease. Once it gains access to epithelial cells, C. jejuni becomes u...
The phylum Actinobacteria harbors many important human pathogens and also provides one of the richest sources of natural products, including numerous antibiotics and other compounds of biotechnological interest. Thus, a reliable phylogeny of this large phylum and the means to accurately identify its different constituent groups are of much interest...
Microbial systematics and phylogeny should form the foundation and guiding light for a comprehensive understanding of different aspects of microbiology. However, there are many critical issues in microbial systematics that are currently not resolved. Some of these include: how to define and delimit a prokaryotic species; development of rationale cr...
Schematic representation of the GC content bias in 696 genomes. The B. dentium Bd1 GC content is circularized.
(0.34 MB TIF)
Predicted transport capabilities of B. dentium Bd1 compared to other bifidobacteria (A). Predicted compounds transported by the sequenced bifidobacteria (B).
(0.43 MB TIF)
Ecological adaptability of B. dentium Bd1 to acidic environments. (A) indicates the intracellular pH of B. dentium Bd1, S. mutans UA159, and Lb. paracasei subsp. paracasei ATCC11974 at various extracellular pH values. The data obtained from three independent experiments were plotted. In (B), growth of B. dentium Bd1 and B. longum subsp. longum ATCC...
Venn diagram of homologs shared between sequenced bifidobacterial genomes. Circle sizes are proportional to members contained in each set.
(0.31 MB TIF)