The Shewanella Blogger

Must-read review on extracellular respiration by Shewanella

shewanella — Tue, 06 Dec 2011 18:32:16 +0000

I just saw this review article by Brutinel and Gralnick on electron shuttling and the role of flavins. For the hardcore Shewanella folks, this will be a must-read paper.

Brutinel ED, Gralnick JA. (2011). Shuttling happens: soluble flavin mediators of extracellular electron transfer in
Shewanella. Appl Microbiol Biotechnol. 2011 Nov 10. [Epub ahead of print]

The genus Shewanella contains Gram negative γ-proteobacteria capable of reducing
a wide range of substrates, including insoluble metals and carbon electrodes. The
utilization of insoluble respiratory substrates by bacteria requires a strategy
that is quite different from a traditional respiratory strategy because the cell
cannot take up the substrate. Electrons generated by cellular metabolism instead
must be transported outside the cell, and perhaps beyond, in order to reduce an
insoluble substrate. The primary focus of research in model organisms such as
Shewanella has been the mechanisms underlying respiration of insoluble
substrates. Electrons travel from the menaquinone pool in the cytoplasmic
membrane to the surface of the bacterial cell through a series of proteins
collectively described as the Mtr pathway. This review will focus on respiratory
electron transfer from the surface of the bacterial cell to extracellular
substrates. Shewanella sp. secrete redox-active flavin compounds able to transfer
electrons between the cell surface and substrate in a cyclic fashion-a process
termed electron shuttling. The production and secretion of flavins as well as the
mechanisms of cell-mediated reduction will be discussed with emphasis on the
experimental evidence for a shuttle-based mechanism. The ability to reduce
extracellular substrates has sparked interest in using Shewanella sp. for
applications in bioremediation, bioenergy, and synthetic biology.

Filed under: General

New paper on Pyruvate/Lactate metabolism in Shewanella

shewanella — Wed, 05 Oct 2011 18:01:29 +0000

I just got the copy of a cool paper recently published in Applied and Environmental Microbiology. I haven’t fully read it yet but it looks really interesting. The main objective is to understand Shewanella‘s aerobic/anaerobic metabolism of lactate, pyruvate, and acetate. There are a number of interesting results and conclusions that should be highly relevant to anyone working with Shewanella. Here is a link to the paper:

Pyruvate and Lactate Metabolism by Shewanella oneidensis MR-1 under Fermentative, Oxygen-limited and Fumarate-Respiring Conditions
Authors: Grigoriy E. Pinchuk, Oleg V. Geydebrekht, Eric A. Hill, Jennifer L. Reed, Allan E. Konopka, Alexander S. Beliaev, and Jim K. Fredrickson
AEM Accepts, published online ahead of print on 30 September 2011

Filed under: General

Site change

shewanella — Mon, 26 Sep 2011 06:42:49 +0000

I added a new page called Q&A. Use this section if you have a question that is not about one of the blog posts. Please contribute to answer too.

I read an interesting Shewanella paper on a solution structure of MtrA. I was really excited when I first saw the paper. But the paper leaves more question than answers. The structure they show in Figure 5 is not really a structure. It looks like a tounge 40 x 30 angstroms in size. It would be nice if they report a pdb file but I don’t think they were able to generate one based on the techniques. Hopefully a crystal structure will be done someday. Here is a link to the paper:

Firer-Sherwood et al. Solution-Based Structural Analysis of the Decaheme Cytochrome, MtrA, by Small-Angle X-ray Scattering and Analytical Ultracentrifugation. J. Phys. Chem. B (2011) vol. 115 (38) pp. 11208-14

Filed under: Cytochromes, General

Tip: conjugation from E. coli to Shewanella at 37˚C

shewanella — Tue, 19 Jul 2011 14:57:00 +0000

Trying to get DNA into Shewanella can be difficult (if you are using a strain other than MR-1). Many of us use conjugation from a special E. coli strain to our particular Shewanella strains (we use ANA-3). I recently tried incubating the mating reaction at 37˚C and to my surprise (not really) we got a lot more “transformed” colonies compared to our usual incubation at 30˚C, which is not ideal for E. coli but good for Shewanella. I think the increased efficiency is because E. coli is more metabolically active and able to conjugate with Shewanella a lot better than at 30˚C. So next time you set up a conjugation reaction put one at 37˚C and see if you get more colonies out of the reaction.

Filed under: General

Breaking News!!!! Decaheme outermembrane cytochrome MtrF structure solved!

shewanella — Tue, 24 May 2011 15:21:11 +0000

You all have to head over to the PNAS website and download the Clarke et al. paper reporting on the crystal structure of MtrF, the MtrC homolog. This cytochrome protein has 10 hemes arranged like a “staggered cross”. To me it looks more like a lightning bolt. It also appears that there is an entry and exit point for electrons… so it is probably not functioning as a capacitor for electrons. There also appears to be a flavin binding site, which supports all the work done in the labs of Gralnick and Bond. The pdb number is: 3PMQ (www.pdb.org). I’m really excited about this paper as it will surely change the way we think about iron reduction, electron transfer to solid substrates, and extracellular respiration.

Link to the PNAS paper by Clarke et al. ”Structure of a bacterial cell surface decaheme electron conduit” (May 23, 2011)

Filed under: Cytochromes

Shewanella CAN grow on sugars

shewanella — Sat, 30 Apr 2011 04:27:19 +0000

This is kind of old news but if you are tired of growing Shewanella on lactate try a carbohydrate like glucose, sucrose, or arabinose… But wait, you need to find out which “candy” your Shewanella can dine on. You can look this up in “Genomic encyclopedia of sugar utilization pathways in theShewanella genus” by Rodionov and colleagues. The paper is open access so enjoy… Heres the reference.

“Genomic encyclopedia of sugar utilization pathways in the Shewanella genus.” Dmitry A Rodionov, Chen Yang, Xiaoqing Li, Irina A Rodionova, Yanbing Wang, Anna Y Obraztsova, Olga P Zagnitko, Ross Overbeek, Margaret F Romine, Samantha Reed, James K Fredrickson, Kenneth H Nealson, and Andrei L Osterman BMC Genomics. 2010; 11: 494. Published online 2010 September 13. doi: 10.1186/1471-2164-11-494.

PMCID: PMC2996990

Filed under: General

Solid paper on gene regulation in Shewanella

shewanella — Wed, 06 Apr 2011 17:52:29 +0000

Those that are tuning in might want to check out the new manuscript on the role of FNR (fumarate-nitrate regulatory) in Shewanella oneidensis MR-1. The paper combines, genetics, transcriptome analysis, and physiology to characterize an fnr deletion strain in MR-1. The Shewanella folks don’t call the Shewanella FNR, FNR. They call it EtrA, electron transport regulator. I guess the latter might be a better name but it does present a lot of confusion in the crowd of folks interested in regulation of anaerobic metabolism. Basically EtrA is FNR. Nevertheless, the paper presents a nice concise analysis of transcriptome changes in the fnr/etrA regulator mutant. The interesting thing about fnr/etrA is that Shewanella can do pretty well without it, although the strain does lag a bit in its growth on nitrate and some other terminal electron acceptors. It’s not dead anaerobically like a crp mutant. That is interesting too because crp and fnr are in the same protein family. The difference is that FNR has a redox active FeS cluster and CRP binds cyclic AMP. Anyway, here is the Pubmed link to the new paper:

Cruz-Garcia C, Murray AE, Rodrigues JL, Gralnick JA, McCue LA, Romine MF, Loffler FE, Tiedje JM. Fnr (EtrA) acts as a fine-tuning regulator of anaerobic metabolism in Shewanella oneidensis MR-1. BMC Microbiol. 2011 Mar 30;11(1):64.

Filed under: Regulation

Iron reduction… the power to dissolve

shewanella — Thu, 06 Jan 2011 05:47:39 +0000

Here is a picture of some serum bottles with Shewanella wild-type and an mtr/omc gene cluster mutant grown in the presence of iron oxide. The third bottle is a “no cell” control. I bet you can’t guess which bottle is the mtr/omc mutant.

I really like this picture because it shows the amazing ability of iron-reducing bacteria to dissolve metal oxides through their metabolism. Imagine if there was a pollutant adsorbed onto the iron. As the iron oxide dissolves so does the pollutant.

cheers…

Filed under: Cytochromes, General

Shewanella citations in 2010

shewanella — Wed, 05 Jan 2011 07:03:47 +0000

I use PubCrawler to auto-search PubMeb everyday for various keywords and title words. I get an email everyday of the search results. One of my search terms is obviously “Shewanella“. This has been a really great tool to keep up to date on the latest papers. Considering it’s a new year, I was curious to know how many papers on Shewanella were published in 2010. After doing a keyword and title word search in Web of Science, I was surprised that there were ~300 papers in that database linked somehow to Shewanella. Is this high or low? Well, I changed the year to 2009, then 2008… and down to 2000 and repeated the title and topic searches. The results are summarized in the table:

Year	Title Search	Keyword Search
2010	84	237
2009	82	231
2008	82	231
2007	91	223
2006	59	168
2005	58	169
2004	47	124
2003	43	119
2002	46	103
2001	28	83
2000	26	73

In the last 10 years we can see the number of Shewanella-related papers increase ~4 times since 2000. That’s pretty good I think. The interest in Shewanella seems to be on the rise. 2010 was definitely a great year for Shewanella with some really great papers. There were some great new discoveries on nanowires, fuel cells, iron reduction, and physiology. For next time, I going to to post my top 5 must-read Shewanella papers of 2010.

Cheers!

Filed under: General

Breaking news about Shewanella’s metabolism

shewanella — Sat, 24 Apr 2010 16:46:56 +0000

So… if you haven’t seen this recent paper by Gralnick’s group, you have to check this out.

Hunt KA, et al. (2010). Substrate-level phosphorylation is the primary source of energy conservation during anaerobic respiration of Shewanella oneidensis strain MR-1 (pubmed link)

This paper showed that Shewanella’s main form of energy conservation under anaerobic conditions comes from substrate level phosphorylation (SLP) and not from oxidative phosphorylation via the ATP synthase. They deleted the genes involved in acetate formation, which liberates an ATP via SLP. If these genes are knocked out then Shewanella no longer grows anaerobically with lactate (e- donor/carbon source) and fumarate (e- acceptor). If you give Shewanella a growth substrate that produces more ATP and higher up in the catabolic pathway, they found that their mutants could grow, but not as good as the wild-type. They then turned their sights on the role of ATP synthase under anaerobic growth conditions. Their results suggest that during anaerobic growth the ATP synthase functions as to generate proton motive force and not in ATP synthesis.

This is a must-read paper for anyone working with Shewanella.

-The Shewanella Blogger.

Filed under: General