Lecture 9 - Microbiomes.docx

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University of Toronto St. George
Cell and Systems Biology
William Navarre

MGY377H © Lisa | Page 13 L E C T U R E 9 : M I C R O B I O M E S TRICHONYMPHA 1. Trichonympha is remarkable in its ability to break down wood as a food source 2. wood & plant cell walls are primarily composed of cellulose 3. cellulose is a polymer of glucose very similar to starch except for the presence of a β(1-4) linkage between every other sugar molecule 1. this enables very tight packing adjacent glycan chains – making it hard for enzymes to access easily 4. starch is composed of glucose molecules connected entirely by α(1-4) linkages & is easy to digest due to its more open packing arrangement 5. Trichonympha carries with it a coat of bacteria that are absolutely essential for it to survive on wood as a primary NRG source 1. they are Trichonympha’s ectosymbionts (a symbiont that lives outside the bacterial cell) 2. these bacteria provide organic N in the form of urea or amino acids that they themselves fix from atmospheric N 2 3. this is critical for the survival of the protist since cellulose is deficient in N, which is critical for the synthesis of nucleotides & amino acids 6. Triconympha also harbour endosymbionts 1. to acquire the complete genome sequence of the endosymbiotic bacteria (TD1) inside Triconympha agilis, Hongoh et al. collected bacterial cells released from a single host protist cell 2. using a strategy known as whole genome amplification &next generation sequencing, they reconstructed the circular bacterial chromosome encoding 761 putative protein-coding genes & 121 pseudogenes 3. the genome indicates the endosymbiont retained the ability to synthesize 15 amino acids and various cofactors 1. this suggests that this bacterial group stably supplies essential nitrogenous compounds deficient in lignocelluloses to their host protists 7. genome sequences can inform us about what metabolic pathways are present or absent in an organism Periplasm (green) & cytoplasm (army green) are shown Blue = synthesized amino acids Red = cofactors Compounds that must be imported are shown in pale colors Nonfunctional pathways and pseudogenes are marked with red X’s MGY377H © Lis| Page 2013 8. Trichonympha is a symbiont in the termite gut 9. due to their metabolic capacity, gut microbes give animals access to otherwise inaccessible food sources HOW GLYCAN METABOLISM SHAPES THE HUMAN GUT MICROBIOTA 1. glycans (polysaccharides) are highly heterogeneous & come from a variety of sources including plants, meat, bacteria, mucous, & milk 2. our own genome only encodes enzymes w the capacity to break down only a few glycans (starch, lactose, sucrose) 3. we rely heavily on microbes to break down a variety of complex glycans BACTEROIDES THETAIOTAOMICRON 4. Bacteroides thetaiotaomicron is a very successful glycophile & an abundant member of our microbiota 1. digests indigestible dietary polysaccharides 2. has a 6.3 Mb genome 3. it encodes the largest ensemble of genes involved in acquiring & metabolizing CHOs 1. includes 163 homologs of 2TonB-dependent outer membrane proteins (SusC & SusD) that bind & import starch, 226 predicted glycoside hydrolases, & 15 polysaccharide lyases 5. by contrast, our 2.85 Gb genome only contains 98 known or putative glycoside hydrolases & is deficient in the enzyme activities required for degradation of xylan-, pectin-, and arabinose-containing polysaccharides that are common components of dietary fibre 6. bacteroides sp. use TonB-dependent transporters & surface/periplasmic enzymes to break large oligosaccharides into simple sugars 1. the TonB-dependent transporter SusC works in concert with the starch-binding lipoproteins SusD, SusE, SusF &SusG (Sus = starch utilization system) 1. SusD, SusE &SusF initiate starch- binding 2. SusG is a glycoside hydrolase α- amylase that breaks down starch 1. SusG carries out initial degradation 3. oligosaccharides are transported into the periplasm via SusC in concert with the inner membrane protein TonB 4. in the periplasm, SusA (aka neopullulanse) & SusB (an α-glucosidase) further degrades malto-oligosaccharides to glucose 5. simple sugars are imported across the inner membrane by an undefined permease(s) 2. homologues of SusC & SusD are a hallmark of every Sus-like system, but CHO-binding proteins akin to SusE & SusF, as well as glycoside hydrolases, vary substantially between Sus-like loci 7. polysaccharides are very complex & require many enzymes for degradation 1. arabinoxylan is a het
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