Sulphoglycolysis in Escherichia coli K-12 closes a gap in the biogeochemical sulphur cycle

Sulphoquinovose (SQ, 6-deoxy-6-sulphoglucose) has been known for 50 years as the polar headgroup of the plant sulpholipid in the photosynthetic membranes of all higher plants, mosses, ferns, algae and most photosynthetic bacteria. It is also found in some non-photosynthetic bacteria, and SQ is part of the surface layer of some Archaea. The estimated annual production of SQ is 10,000,000,000 tonnes (10 petagrams), thus it comprises a major portion of the organo-sulphur in nature, where SQ is degraded by bacteria. However, despite evidence for at least three different degradative pathways in bacteria, no enzymic reaction or gene in any pathway has been defined, although a sulphoglycolytic pathway has been proposed⁷. Here we show that Escherichia coli K-12, the most widely studied prokaryotic model organism, performs sulphoglycolysis, in addition to standard glycolysis. SQ is catabolised through four newly discovered reactions that we established using purified, heterologously expressed enzymes: SQ isomerase, 6-deoxy-6-sulphofructose (SF) kinase, 6-deoxy-6-sulphofructose-1-phosphate (SFP) aldolase, and 3-sulpholactaldehyde (SLA) reductase. The enzymes are encoded in a ten-gene cluster, which probably also encodes regulation, transport and degradation of the whole sulpholipid; the gene cluster is present in almost all (>91%) available E. coli genomes, and is widespread in Enterobacteriaceae. The pathway yields dihydroxyacetone phosphate (DHAP), which powers energy conservation and growth of E. coli, and the sulphonate product 2,3-dihydroxypropane-1-sulphonate (DHPS), which is excreted. DHPS is mineralized by other bacteria, thus closing the sulphur cycle within a bacterial community.

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Identification of a conserved branched RNA structure that functions as a factor-independent terminator

All cells regulate which regions of DNA are transcribed to RNA. Controlling where transcription terminates is an essential part of this regulation. In bacterial cells, RNA structures, referred to as factor-independent terminators, can interact with RNA polymerase to direct termination. These structures are typically inverted sequence repeats that form an RNA hairpin followed by several uridine residues. We identified a branched RNA structure that functions as a factor-independent terminator. The terminated product is a functional small RNA, but termination is inefficient, allowing transcription of downstream genes. Additional branched terminators are encoded in bacterial chromosomes, demonstrating that this unusual terminator is not unique. This work reveals an unappreciated structural diversity of factor-independent terminators and will inform annotation of bacterial genomes.    

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A new metabolic cell-wall labelling method reveals peptidoglycan in Chlamydia trachomatis

Peptidoglycan (PG), an essential structure in the cell walls of the vast majority of bacteria, is critical for division and maintaining cell shape and hydrostatic pressure. Bacteria comprising the Chlamydiales were thought to be one of the few exceptions. Chlamydia harbour genes for PG biosynthesis and exhibit susceptibility to ‘anti-PG’ antibiotics yet attempts to detect PG in any chlamydial species have proven unsuccessful (the ‘chlamydial anomaly’). We used a novel approach to metabolically label chlamydial PG using d-amino acid dipeptide probes and click chemistry. Replicating Chlamydia trachomatis were labelled with these probes throughout their biphasic developmental life cycle, and the results of differential probe incorporation experiments conducted in the presence of ampicillin are consistent with the presence of chlamydial PG-modifying enzymes. These findings culminate 50 years of speculation and debate concerning the chlamydial anomaly and are the strongest evidence so far that chlamydial species possess functional PG.

Fig. 1. Fluorescent labelling of intracellular C. trachomatis PG. 

a–e, Differential interference contrast (DIC) (a) and fluorescent (b–e) microscopy of L2 cells infected for 18 h with C. trachomatis in the presence of the dipeptide probe EDA-DA (1 mM). Subsequent binding of the probe to an azide modified Alexa Fluor 488 (green) was achieved via click chemistry. Antibody to MOMP (red) was used to label chlamydial EBs and RBs. DAPI (blue) was used for nuclear staining. b–e show a merge of all three fluorescent channels. Boxes indicate location of chlamydial inclusions, and magnification of the boxes is provided in c–e. Fluorescent images are maximum intensity projections of deconvoluted z-stacks. 

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Different walls for rods and balls: the diversity of peptidoglycan

Peptidoglycan performs the essential role of resisting turgor in the cell walls of most bacteria. It determines cell shape, and its biosynthesis is the target for many important antibiotics. The fundamental chemical building blocks of peptidoglycan are conserved: repeating disaccharides cross-linked by peptides. However, these blocks come in many varieties and can be assembled in different ways. So beyond the fundamental similarity, prodigious chemical, organizational and architectural diversity is revealed. Here, we track the evolution of our current understanding of peptidoglycan and underpinning technical and methodological developments. The origin and function of chemical diversity is discussed with respect to some well-studied example species. We then explore how this chemistry is manifested in elegant and complex peptidoglycan organization and how this is interpreted in different and sometimes controversial architectural models. We contend that emerging technology brings about the possibility of achieving a complete understanding of peptidoglycan chemistry, through architecture, to the way in which diverse species and populations of cells meet the challenges of maintaining viability and growth within their environmental niches, by exploiting the bioengineering versatility of peptidoglycan.

Peptidoglycan architecture in B. subtilis, S. aureus and E. coli.

A. Metrics of peptidoglycan for comparison. Ranges are lowest and highest values identified in the literature (Vollmer and Seligman, 2010; Wheeler et al., 2011). In S. aureus and E. coli these are average values, in B. subtilis they are a representative of the overall range.

B. AFM gallery of sacculi comprising images comprising multiple sacculi per field, and key architectural details specific to each species (Hayhurst et al., 2008; Turner et al., 2010; 2013).

C. Interpretive diagrams drawn from yellow rectangles marked in ‘B’.

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Why the bacterium Oenococcus oeni is vital for a good glass of wine

Wine is produced by the alcoholic fermentation of the sugars in grape juice by yeasts. There are secondary fermentations, usually carried out by the bacterium Oenococcus oeni, which produce flavour/aroma compounds which add to the overall quality of the wine. In a new article published in Open Biology, researchers have constructed a proteomic map of O. oeni ATCC BAA-1163 and, by comparison with maps of related strains, have identified a series of proteins that could be of importance in the secondary fermentation of wine. This proteomic map will form an important basis for the future production of high quality wine.

Reference two-dimensional gels from protein preparations. Total protein (a) and membrane (b) fractions obtained from extract of O. oeni ATCC BAA-1163 were analysed in two-dimensional gels, by the use of a nonlinear pH gradient (pH 3.0–11.0) and the second dimension ranging from 150 to 10 kDa.

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You Are What You Host: Microbiome Modulation of the Aging Process

As you look in the mirror, you may only see yourself staring back,but in reality, you are not alone; you share your body with trillions of others. Contained on and within our bodies thrives a dynamic population of microbes that form a ‘‘metaorganism’’ comprising ten bacterial cells for every one of our own. 

Despite coevolving in the presence of this ‘‘microbiome’’ for 500 million years (Cho and Blaser, 2012), only recently have advances in sequencing technology allowed us to appreciate the complexities of this relationship and the manner by which genomes within metaorganisms interact and affect one another. Interindividual variations in the

microbiome impact multiple human pathologies, from metabolic syndrome to cancer (Cho and Blaser, 2012). However, new datain invertebrate systems indicate that microbes extend their effects beyond host pathology to systemic modulation of the rate of aging.

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La dieta cambia rápidamente nuestra flora intestinal

Trabajo de Nature (23 Enero 2014)

Long-term dietary intake influences the structure and activity of the trillions of microorganisms residing in the human gut, but it remains unclear how rapidly and reproducibly the human gut microbiome responds to short-term macronutrient change. Here we show that the short-term consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression. The animal-based diet increased the abundance of bile-tolerant microorganisms (Alistipes, Bilophila and Bacteroides) and decreased the levels of Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium rectale and Ruminococcus bromii). Microbial activity mirrored differences between herbivorous and carnivorous mammals, reflecting trade-offs between carbohydrate and protein fermentation. Foodborne microbes from both diets transiently colonized the gut, including bacteria, fungi and even viruses. Finally, increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids and the outgrowth of microorganisms capable of triggering inflammatory bowel disease. In concert, these results demonstrate that the gut microbiome can rapidly respond to altered diet, potentially facilitating the diversity of human dietary lifestyles.

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