"Phylogeny driven approaches to genomics and metagenomics": slides w/ audio from my talk at #UCDavis 1/29

Gave a talk here at UC Davis last week. Alas, not my best talk – too rushed. But, anyway, here is a video of the slideshow w/ audio. Title “Phylogeny driven approaches to genomics and metagenomics”


Worth a look: PhyloFacts FAT-CAT web server: ortholog identification & function prediction

Quick post.  This seems like a potentially useful resource and tool: The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification

The PhyloFacts ‘Fast Approximate Tree Classification’ (FAT-CAT) web server provides a novel approach to ortholog identification using subtree hidden Markov model-based placement of protein sequences to phylogenomic orthology groups in the PhyloFacts database. Results on a data set of microbial, plant and animal proteins demonstrate FAT-CAT’s high precision at separating orthologs and paralogs and robustness to promiscuous domains. We also present results documenting the precision of ortholog identification based on subtree hidden Markov model scoring. The FAT-CAT phylogenetic placement is used to derive a functional annotation for the query, including confidence scores and drill-down capabilities. PhyloFacts’ broad taxonomic and functional coverage, with >7.3 M proteins from across the Tree of Life, enables FAT-CAT to predict orthologs and assign function for most sequence inputs. Four pipeline parameter presets are provided to handle different sequence types, including partial sequences and proteins containing promiscuous domains; users can also modify individual parameters. PhyloFacts trees matching the query can be viewed interactively online using the PhyloScope Javascript tree viewer and are hyperlinked to various external databases. The FAT-CAT web server is available at http://phylogenomics.berkeley.edu/phylofacts/fatcat/.

Sign up: SMBE Satellite Mtg. on Eukaryotic-Omics 4/29-5/2 at #UCDavis

Going to be good:

Eukaryotes | SMBE Satellite Meeting on Eukaryotic -Omics – April 29 to May 2, UC Davis Conference Center

No bias here – given that it is organized by Holly Bik in my lab and it is at UC Davis. The lineup of speakers is great and the topic is timely.  So sign up  …


Rachel Adams UC Berkeley Groundtruthing next-gen sequencing for microbial ecology: is beta diversity robust to errors in pyrosequencing?
Nicholas A. Bokulich UC Davis Regional Patterns in Grape Fungal Consortia Define Wine Fermentation Communities
Sara Branco UC Berkeley Fungi at a small-scale: spatial zonation of fungal assemblages around single trees
C. Titus Brown Michigan State University Sequencing and assembly of diverse eukaryotes: like metagenomics, but much harder
Peter Countway Bigelow Laboratory for Ocean Sciences Title TBA
Simon Creer Bangor University, Wales Title TBA
Tom Delmont Marine Biological Laboratory, Woods Hole Phaeocystis antarctica spatiotemporal diversity, activity and its relation to prokaryotes and viruses using physiological and ‘omic approaches
Jonathan Eisen UC Davis The need for a phylogeny driven genomic encyclopedia of eukaryotes
Laura Eme Dalhousie University Large scale phylogenomic analyses of Blastocystis subtype 1 reveals a major role for lateral gene transfer in adaptation to parasitism of the human gut
Jack Gilbert Argonne National Lab Addressing microbial eukaryotic biogeography in home, hospitals and the world
Jean-David Grattepanche Smith College Title TBA
Victor Hanson-Smith UC San Francisco Identifying Loci of Functional Evolution in Ancestral Genes
Ian King University of Guelph Biomonitoring 2.0: A high-throughput genomics approach for comprehensive biological assessment of environmental change
Andrew Krohn Northern Arizona University Rhizosphere microbial community dynamics of drought-stressed pinyon pines (Poster)
Franck Lejzerowicz University of Geneva Exploring the deep-sea foraminiferal diversity by multiplexed RNA and DNA-based ultra-deep sequencing and ultra-fast bioinformatic analyses
Matthew Morgan CSIRO Australia Next-generation sequencing reveals the impacts of inundation and drought on eukaryote biodiversity in semi-arid floodplain soils
Laura Wegener Parfrey University of Colorado, Boulder Incorporating microbial eukaryotes into analyses of the human microbiome
Katherine Pollard UC San Francisco Title TBA
Dorota Porazinska University of Florida Discrimination of microscopic pests of agricultural importance with NGS
Thomas Richards NHM London Title TBA
Surya Saha Cornell University Composition of the Maize Endophytic Microbiome is Correlated with Maize Genotype (Poster)
Søren Sørensen University of Copenhagen Title TBA
Fabian Staubach Stanford University Host species and environmental effects on bacterial communities associated with Drosophila in the laboratory and in the natural environment
Sarah Stephenson CSIRO Australia Metagenetic examinations of benthic eukaryl estuarine communities
Joshua Stern Georgia Institute of Technology Searching for the Phylogenetic Place of Eukaryotes, Using Data from STORI
W. Kelley Thomas University of New Hampshire Title TBA
Xianfa Xie Virginia State University Comparative genomic study of the origin and evolution of eukaryotes

Guest post from Kimmen Sjölander about FAT-CAT phylogenomics pipeline

Below is a guest post from my friend and colleague Kimmen Sjölander, Prof. at UC Berkeley and phylogenomics guru. 

Announcing the FAT-CAT phylogenomic annotation webserver.

FAT-CAT is a new web server for phylogenomic prediction of function and ortholog identification and for taxonomic origin prediction of metagenome sequences based on HMM-based classification of protein sequences to >93K pre-calculated phylogenetic trees in the PhyloFacts database. PhyloFacts is unique among phylogenomic databases in having both broad taxonomic coverage – more than 7.3M proteins from >99K unique taxa across the Tree of Life, including targeted coverage of genomes from Eukaryotes, Bacteria and Archaea — and integrating functional data on trees for Pfam domains and multi-domain architectures. PhyloFacts trees include functional and annotation data from UniProt (SwissProt and TrEMBL), GO, BioCyc, Pfam, Enzyme Commission and other sources. The FAT-CAT pipeline uses HMMs at all nodes in PhyloFacts trees to classify user sequences to different levels of functional hierarchies, based on the subtree HMM giving the sequence the strongest score. Phylogenetic placements within orthology groups defined on PhyloFacts trees are used to to predict function and to predict orthologs. Sequences from metagenome projects can be classified taxonomically based on the MRCA of the sequences descending from the top-scoring subtree node. Because of the broad taxonomic and functional coverage, FAT-CAT can identify orthologs and predict function for most sequence inputs. We’re working to make FAT-CAT less computationally intensive so that users will be able to upload entire genomes for analysis; in the interim, we limit users to 20 sequence inputs per day. Registered users are given a higher quota (see details online). We’d love to hear from you if you have feature requests or bug reports; please send any to Kimmen Sjölander – kimmen at berkeley dot edu (parse appropriately). 

Worth a read: Jim Staley on a "Universal Species Concept" and the history of microbial species concepts

Interesting paper came up in my automated google searches for “phylogenomics”: Transitioning Toward a Universal Species Concept for the Classification of all Organisms | InTechOpen.  It is by Jim Staley who has been writing a lot about microbial species concepts in the last few years.  In addition to trying to bridge the gap between bacteria/archaea and eukaryotes in terms of species concepts.  Not sure how I feel about everything in the paper but it has a really nice history of how species have been defined for bacteria. He breaks down this history into four periods

  • Discovery of microorganisms,
  • Advent of pure cultures and phenotypic features,
  • Introduction of molecular analyses and
  • Gene sequencing and genomics.
And goes through a bit of detail on each one.  He also discusses what he sees as a need for a universal species concept and even makes some suggestions about how it might be implemented.  Definitely worth a read.  
Some related posts of mine and or links of potential interest:

Slides and slideshow w/ audio from my talk at Bay Area Illumina User’s Meeting

Just quick post … gave a talk Thursday at the Bay Area Illumina User’s meeting.  I have posted my slides to Slideshare and a Video Slideshow with audio to Youtube.

Three talks, 1.5 days at #ISMB … phylogeny, phylogenomics, open science and more

Gave three talks in 1.5 days here in Long Beach as part of the satellite meetings associated with the “Intelligent Systems for Molecular Biology” (ISMB) 2012 Conference. I will write more about the meeting and the craziness of giving three very different talks in 1.5 days. But for now I wanted to at least get my talks posted here since I posted the slides to slideshare and recorded the audio in synch with the slides and posted these “slideshows” to YouTube. Here are the talks below:

Talk 1 for the “Bioinformatics Open Source Conference” BOSC2012.  Was asked to talk about Open Science … so … I did …

Slideshow with audio:

Talk 2 for the Student Council Symposium SCS2012. Sort of supposed to be a career guidance discussion so I geared my talk on the lines of “lessons learned” …

Slideshow with audio:

Talk 3 for the “Automated function prediction” AFP2012 satellite meeting.  I decided to talk about phylogenetic and phylogenomics approaches to functional prediction …

Slideshow with audio:

http://storify.com/phylogenomics/jonathan-eisen-talks-at-ismb-satellite-meetings.js[<a href=”http://storify.com/phylogenomics/jonathan-eisen-talks-at-ismb-satellite-meetings” target=”_blank”>View the story “Jonathan Eisen @phylogenomics talks at #ISMB Satellite Meetings” on Storify</a>]

BABS meeting at #UCDavis – “Phylogenomics and Systematics”

(Please respond to psward@ucdavis.edu if you plan to attend)


Tuesday evening, 22 May 2012

at UC Davis, 1022 Life Sciences Building


The genomics era holds great promise (and challenge) to systematics. There is the prospect of generating sequence data that will provide unprecedented resolution of phylogenetic relationships across the Tree of Life, and a much improved understanding of the tempo and mode of evolution. Join us for two talks on phylogenomics, along with plenty of discussion, leavened by pizza and beer.

Featuring presentations by…

HOLLY BIK, Postdoctoral Researcher, Eisen Lab, UC Davis Genome Center

“Phylogeny-based taxonomy assignments from environmental metagenome data” (Note updated title)


BASTIEN BOUSSAU, Postdoctoral Fellow, Huelsenbeck Lab, UC Berkeley

“Methods of phylogenetic inference for genome-scale data sets”

Schedule and venue:
5:30 pm: social gathering with beverages (beer and soft drinks) and informal
pizza dinner: cost ca. $10, to be collected at door, 1022 Life Sciences, UC Davis campus.
7:00 – 9:00 pm: talks, followed by discussion, in same room.

Reservations required for beverages and dinner (but not the talk). Please email reservations to your host, Phil Ward: psward@ucdavis.edu by Sunday, May 20

For a map of UC Davis campus and Life Sciences Building:

Parking is available in the West Entry Parking Structure, immediately west of Life Sciences. If coming from the Bay Area take the Hwy. 113 exit off I-80, and then the first exit off Hwy 113, which is Hutchison Drive. This will bring you directly to the parking garage. Or, as Google Maps would say:

All are welcome, members or not. If you want to join the Biosystematists, sign up for our mailing list at:

See you in Davis!


The Axis of Evol: Getting to the Root of DNA Repair with Philogeny

The Axis of Evol: Getting to the Root of DNA Repair with Philogeny 
In 2005 I wrote an essay about my time in graduate school that was potentially going to be included in a special issue of Mutation Research in honor of my PhD advisor Phil Hanawalt.  Alas, publishing my essay ran into complications in regard to the closed access policies of this journal.  So in the end, my essay was not published.  I had forgotten about it mostly until very recently.  And so I decided to convert the essay to a blog post.  The essay is sort of about what I did in grad. school and sort of about Phil …
Phylogenomics is a field in which genome analysis and evolutionary reconstructions are integrated. This integration is important because genome data is of great value in evolutionary reconstructions, because evolutionary analysis is critical for understanding and interpreting genomic data, and because there are feedback loops between evolutionary and genome analysis such that they need to be done in an integrated manner. In this paper I describe how I developed my particular phylogenomic approach under the guidance of my Ph.D advisor Philip C. Hanawalt. Since I was the first to use the term phylogenomics in a publication, I have decided to rename the field (at least temporarily) Philogenomics.
1. Doctor of Philosophy
When I went to Stanford for graduate school, I was interested in combining evolutionary analysis and molecular biology in a way that would allow me to study molecular mechanisms through an evolutionary perspective. Although I had gone to Stanford ostensibly to work on butterfly population genetics, within two days of starting a rotation in Phil’s lab, I knew that that was where I wanted to work. This decision was somewhat traumatic, since the work on butterflies included spending the summers at 10,000 feet in the Rocky Mountains and possibly chasing butterflies like a Nabakov wanna-be all over the mountain ranges of the world. As an avid outdoor person, this was quite appealing. Nevertheless, I chose to spend 99% of my graduate work in the dingy confines of Herrin Hall, studying DNA repair. The choice of joining Phil’s lab did have one very positive affect – and that was on my relationship with my grandfather on my mother’s side. Benjamin Post was in many ways like a father to me, especially after my father passed away. He was a physicist from the “old school” and thought that most of biology was completely useless. Needless to say, when I told him I was going to graduate school in California (which he considered already one strike against me) to study butterflies, he decided I was simply a lost cause. Despite all his talk of Einstein and computers and math when I was a child, I might as well have been a poet from his point of view. To make matters worse, my grandfather was a crystallographer, and my brother was getting his Ph.D in crystallography at Harvard. When I informed my grandfather that I was going to be working on DNA repair, he seemed somewhat interested. And then I told him, my advisor, Phil Hanawalt, is relatively well known, and actually used to be considered a biophysicist. Then my grandfather really perked up. He said, “Hanawalt – is he related to Don Hanawalt?” It turns out, that my grandfather worked in the same field as Phil’s father (they both did powder diffraction) and knew him. So my grandfather said “You may not be doing real science, but at least you are doing it with the relative of a real scientist.” Thankfully, I was no longer the black sheep in the family. So, with my grandfather’s approval, I embarked on a career in DNA repair.

I would like to add that I was very torn in writing this article. On the one hand, Phil was the greatest advisor I could ever imagine, allowing me to pursue studies on the evolution of DNA repair and comparative genomic analysis, even though nobody else in the lab worked on such things and at times, nobody seemed interested in them either. Phil’s support allowed me to explore my own interests and develop my concepts for the idea of “Phylogenomics” or the combining of evolutionary reconstructions and genome analysis. On the other hand, this special issue is being published in an Elsevier journal. As a supporter of the Open Access movement on scientific publications (see http://www.plos.org) and the brother of one of the founders of the Public Library of Science, publishing in an Elsevier journal is like cavorting with the devil. But the pull of Phil is very strong (some strange sort of force actually) and despite the effects that this may have on my relationship with my brother, I have agreed to publish in this special issue, and thus can now say that I sold my soul for Phil Hanawalt. [[OOPS – Spoke too soon on this when I wrote it — in the end I just could not sign on the dotted line]].
In this essay, I describe my development in Phil’s lab of the idea of “Phylogenomics” or the combination of evolutionary reconstructions and genome analysis. I would like to add that this is not an attempt to review the field of phylogenomics or all the studies that could be called phylogenomics of DNA repair. For that I recommend reading other papers by myself (some of which are discussed below) as well as those by Rick Wood [1-4]}, Janusz M Bujnicki [5], Eugene Koonin [6-14]}, Carlos Menck [15-18], Michael Lynch [19-21], Patrick Forterre [22-24], Nancy Moran [25-29], and others. This is just meant to review my angle on the phylogenomics of repair and Phil’s contribution to this.
2. RecAgnizing the value of evolutionary analysis in studies of DNA repair
A post-doc in Phil’s lab at the time I was there, Shi-Kau (now known as Scott) Liu was working on analysis of some studies of recA mutants he had done while working in Irwin Tessman’s lab. He asked me if I could help him with some comparative analyses of RecA protein sequences from different species, in the hopes that this might help interpret his experimental data. We then downloaded and aligned all available RecA protein sequences from different species of bacteria and compared the sequence variation to the recently solved crystal structure of a form of the E. coli RecA protein. Specifically we were looking for compensatory mutations in which there was a change in one amino-acid in the region there was a correlated change in another amino-acid in the same region (these were detected using an evolutionary method called character-state reconstruction).  Interestingly, in some regions of the crystal structure (e.g., the monomer-monomer contact regions) extensive compensatory mutations could be detected, suggesting that this region of the crystal was conserved between species. In other regions of the crystal (e.g., the filament-filament contact regions), no compensatory mutations could be detected suggesting either that this region of the structure was not conserved between species or that the filament contact regions were some artifact of crystallization. This was important to show since the mutations Shi-Kau was looking at were suppressors of another recA mutant (recA1202) and the suppressors we found did not make complete sense if the filament-filament contact regions of the crystal reflected perfectly what was going on in-vivo (30).
In this way, evolutionary reconstructions helped inform experimental studies in E. coli. While this concept was not necessarily novel, it is important to point out that most molecular sequence comparisons used for structure-function studies both then and now focus on sequence conservation (that is, what is identical or similar between sequences). This does not take full advantage of the evolutionary history of sequences since it does not specifically examine how the sequence conservation came to be (that is, it does not look at the amino-acid changes that occurred, just what is conserved). This made me realize that comparative analysis (identifying what is similar or different between genes or species) was fundamentally different from evolutionary reconstructions (which can identify how and possibly even why the similarities and differences came into being). I should point out that to do the compensatory mutation analysis well requires lots of sequences and this was one of the hidden reasons behind why I have pushed for ten years for people studying the evolutionary relationships among microbes to use recA as a marker as they use rRNA (31).
3. Sniffing around at homologs of repair genes
Shortly after the recA analysis was complete, another problem being addressed in the Hanawalt lab presented an even more powerful test for evolutionary reconstructions. Kevin Sweder, another post-doc in the lab, was working on yeast strains with defects in homologs of human DNA repair genes. It was at this time that many of the human DNA repair genes were being cloned and shown to be members of the helicase superfamily of proteins. Many of these could further be assigned to one particular subfamily within the helicase superfamily – the subfamily that contained the yeast SNF2 protein. Proteins in the SNF2 family could be readily identified because their helicase-like domains were all much more similar to each other than any were to other helicase-domain containing proteins. Yet many scientists, including Kevin, were presented with a problem. As the yeast genome was being completed, blast searches could identify that yeast encoded many proteins in the SNF2 family. However, these same blast searches could not readily identify which yeast gene was the orthologs of which human gene. For those who do not know, homologous genes or proteins come in two primary forms – paralogs, which are genes related by gene duplications (e.g., alpha and beta globin) and orthologs, which are the same form of a gene in different species (e.g., human and mouse alpha-globin). Thus if one wanted to use yeast as a model to study a human disease due to a mutation in a SNF2 homolog, it would be helpful to know which yeast gene was the ortholog of the human gene of interest. Since paralogs are related to each other by duplication events and since duplication events are an evolutionary event, I figured that an evolutionary tree of the SNF2 family proteins might help divide the gene family into groups of orthologs.
Indeed, this is exactly what we found – the SNF2 family could be divided into many subfamilies, each of which contained a human and a yeast gene and thus these genes could be considered orthologs of each others. In our analysis we found something even more striking. For every subfamily in the SNF2 superfamily, if the function of more than one member of the subfamily was known (e.g., the human and yeast genes), the function was always conserved. Also, all different subfamilies appeared to have different functions (32). Thus one could predict the function of a gene by which subfamily in which it resided. As with the analysis of RecA, it should be pointed out that the phylogenetic tree-based assignment of genes to subfamilies was more useful than blast searches because blast is simply a way to identify similarity among genes/proteins. The tree allows one to group genes into correct subfamilies even if rates and patterns of evolution have changed over time and are different in different groups. Again, this is a distinction between comparative analysis and evolutionary analysis.
4. A gut feeling leads to the idea of “Phylogenomics”
With the SNF2 analysis as a backdrop, I proceeded to proselytize to anyone who would listes, that phylogenetic trees of genes were going to revolutionize genomic sequencing proteins by allowing one to predict the functions of many unknown genes. Genome sequencing projects of course product lots of sequence data and little functional information. Although most of the people in the Hanawalt lab (except maybe Phil) could not have cared less about my evolutionary rantings, fortunately for me, one person called my bluff. Rick Myers, a professor in the Stanford Medical School and one of the heads of the Stanford Human Genome Center was asked to write a News and Views for Nature Medicine about the recent publications of the genomes of E. coli O157:H7 and Helicobacter pylori. So Rick challenged me and said I should try and come up with a real example of how the people who worked on these genomes screwed something up by not doing an evolutionary analysis. Fortunately, it was easy to find an interesting case to study in one of the genomes. In the H. pylori paper, the authors had predicted that the species should have mismatch repair but then reported something quite unusual – the genome encoded a homolog of MutS but did not encode a homolog of MutL. I suppose this should have raised a red-flag to them since all species known to have mismatch repair required homologs of both of these proteins for the process. While some species had other bells and whistles (e.g., the use of MutH and Dam in gamma proteobacteria), the use of MutS and MutL was absolutely conserved. An evolutionary tree of the MutS homologs available at the time including the one in H. pylori also suggested a red-flag should have been raised before predicting that this species possessed mismatch repair.
The MutS family in prokaryotes could be divided into two separate subfamilies, which I called MutS1 and MutS2. All genes known to be involved in mismatch repair were in the MutS1 family. No gene in the MutS2 family had a known function. The H. pylori gene was in the MutS2 family. So this species had no MutL and a MutS homolog in a novel subfamily. To us, this suggested that it would be a bad idea to predict the presence of mismatch repair in this species (33). Later, I showed that there was a general trend – all prokaryotes with just a MutS2-like protein did not have a MutL-homolog, and all species with a MutS1-like protein did (34-36). Experimental work has now shown that the MutS2 of H. pylori is not involved in MMR and that this species apparently does not have any MMR (37). This is important because this apparently causes this species to have an exceptionally high mutation rate, which in turn can effect how one designs vaccines and drugs and diagnostics to target it. It should be pointed out that the role of the MutS2 homologs is not known although they have been knocked out in many species and as of yet none have a role in MMR. Thus predicting function by evolutionary analysis (or more specifically, not incorrectly predicting function) can be of great practical value.
      It is from this analysis that I came up with the idea of “Phylogenomics” or the integration of evolutionary reconstructions and genome analysis (34-36). These approaches should be fully integrated because there is a feedback loop between them such that they cannot be done separately. For example, in the studies of MutS and MutL it is necessary to do a genome analysis to identify the presence or absence of homologs of these genes, then an evolutionary analysis to determine which forms of each of the genes are present, then a genome analysis again to determine the number and combination of different forms and then an evolutionary analysis to determine whether and when particular forms were gained and lost over evolutionary time, and so on. 
5. Lions and TIGRs and bears
Since leaving Phil’s lab I have been a faculty member at The Institute for Genomic Research (TIGR) and in that time we have found dozens of new uses for a phylogenomic approach and designed many new methods to implement phylogenomics. Such an approach has led to many interesting findings relating to DNA repair. Phylogenetic analysis of eukaryotic genomes has allowed us to identify many nuclear encoded genes that are homologs of DNA repair genes but appear to evolutionary derived from the organellar genomes and thus are good candidates for still having a role in DNA repair in the organelles (38). These include both putatively plastid-derived genes (encoding RecA, Mfd, Fpg, RecG, MutS2, Phr, Lon) and mitochondrial-derived genes (encoding RecA, Tag). Interestingly the presence of Mfd but not UvrABCD is also found in many endosymbiotic bacteria, although the explanation for what this Mfd might be doing is unclear. Phylogenomic analysis has allowed us to identify the loss of important DNA repair genes in various species such as the apparent loss of all the genes for non-homologous end joining in the causative agent of malaria, Plasmodium falciparum (39). An important component of this analysis was the finding that this species did not have an orthologs of DNA ligase IV, even though the original annotation of the genome had suggested it did (Figure 1). 
Figure 1. Phylogenetic tree of DNA ligase homologs showing the presence of an orthologs of DNA Ligase I in Plasmodium falciparum but no orthologs of DNA ligase IV, consistent with the absence of non homologous end joining. 
Among the other interesting repair-related features we have found are: the presence of two MutL homologs in an intracellular bacteria Wolbachia pipientis wMel (40), the presence of two UvrA homologs in Deinococcus radiodurans (41) and Chlorobium tepidum (42), the absence of MutS and MutL from Mycobacterium tuberculosis(43), and the presence of multiple ligases for each chromosome in Agrobacteriumtumefaciens (44). Continued surprises come from almost every genome.
However, all is not good in the world of phylogenomics. One of the biggest problems is that most of the experimental studies of DNA repair that have formed the basis of out knowledge in the field have been done in a narrow range of species. For example, there are estimated to be over 100 major divisions of bacteria (Phyla) and of these, most DNA repair studies have been restricted to three of these phyla (Proteobacteria, Firmicutes (also known as lowGC Gram-positives), and Actinobacteria (also known as highGC Gram positives). This means that if anything novel evolved in any of the other lineages, we would not know about it. This probably explains why, when we sequenced the genome of the radiation resistant bacteria D. radiodurans, analysis of the homologs of DNA repair genes in the genome did reveal many homologs of known repair genes but this list did not have many features that were unusual compared to non radiation resistant species (Table 1) and thus was not of much use in understanding what makes this species so resistant (41).
Table 1. Homologs of known DNA repair genes identified in the initial analysis of the D. radiodurans genome sequence
Genes in D. radiodurans
Unusual features
Nucleotide Excision Repair
UvrABCD, UvrA2
UvrA2 not found in most species
Base Excision Repair
AlkA, Ung, Ung2, GT, MutM, MutY-Nths, MPG
More MutY-Nths than most species
AP Endonuclease
Mismatch Excision Repair
MutS, MutL
   Migration and resolution
RuvABC, RecG
PolA, PolC, PolX, phage Pol
PolX not in many bacteria
dNTP pools, cleanup
MutTs, RRase
LexA, RadA, HepA, UVDE, MutS2
UvDE not in many bacteria

 This of course means that genome sequencing and analysis, even if done in a robust way, only works well if there is a core of experimental studies on which to base the analysis.
In the end, I would like to define a new word – philogenomics which is the combination of studies of evolution, genomics, DNA repair, thymine metabolism, and punning. The ultimate proof of a philogenomic approach, of course, will come when it figures out the mechanism underlying thymineless death. But that is another story.
6. Acknowledgements
I would like to thank Philip C. Hanawalt for his support during and after my Ph.D research in his lab. Everyone in the field knows he is a great scientist. What they may not all know is that he is an even better human being.
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[3]       Wood, R.D. and M.K. Shivji, Which DNA polymerases are used for DNA-repair in eukaryotes? Carcinogenesis, 1997. 18(4): p. 605-610.
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[15]     Menck, C.F., Shining a light on photolyases. Nat Genet, 2002. 32(3): p. 338-9.
[16]     Simpson, A.J., et al., The genome sequence of the plant pathogen Xylella fastidiosa. The Xylella fastidiosa Consortium of the Organization for Nucleotide Sequencing and Analysis. Nature, 2000. 406(6792): p. 151-7.
[17]     Morgante, P.G., et al., Functional XPB/RAD25 redundancy in Arabidopsis genome: characterization of AtXPB2 and expression analysis. Gene, 2005. 344: p. 93-103.
[18]     Martins-Pinheiro, M., et al., Different patterns of evolution for duplicated DNA repair genes in bacteria of the Xanthomonadales group. BMC Evol Biol, 2004. 4(1): p. 29.
[19]     Estes, S., et al., Mutation accumulation in populations of varying size: the distribution of mutational effects for fitness correlates in Caenorhabditis elegans. Genetics, 2004. 166(3): p. 1269-79.
[20]     Denver, D.R., et al., Mutation rates, spectra, and hotspots in mismatch repair-deficient Caenorhabditis elegans. Genetics, 2005.
[21]     Denver, D.R., S.L. Swenson, and M. Lynch, An evolutionary analysis of the helix-hairpin-helix superfamily of DNA repair glycosylases. Mol Biol Evol, 2003. 20(10): p. 1603-11.
[22]     Forterre, P., Displacement of cellular proteins by functional analogues from plasmids or viruses could explain puzzling phylogenies of many DNA informational proteins. Mol Microbiol, 1999. 33(3): p. 457-65.
[23]     Cohen, G.N., et al., An integrated analysis of the genome of the hyperthermophilic archaeon Pyrococcus abyssi. Mol Microbiol, 2003. 47(6): p. 1495-512.
[24]     Bouyoub, A., et al., A putative SOS repair gene (dinF-like) in a hyperthermophilic archaeon. Gene, 1995. 167(1-2): p. 147-149.
[25]     Moran, N.A. and A. Mira, The process of genome shrinkage in the obligate symbiont Buchnera aphidicola. Genome Biol, 2001. 2(12): p. RESEARCH0054.
[26]     Dale, C., et al., Loss of DNA recombinational repair enzymes in the initial stages of genome degeneration. Mol Biol Evol, 2003. 20(8): p. 1188-94.
[27]     van Ham, R.C., et al., Reductive genome evolution in Buchnera aphidicola. Proc Natl Acad Sci U S A, 2003. 100(2): p. 581-6.
[28]     Moran, N.A. and J.J. Wernegreen, Lifestyle evolution in symbiotic bacteria: insights from genomics. Trends in Ecology and Evolution, 2000. 15(8): p. 321-326.
[29]     Moran, N.A., Accelerated evolution and Muller’s rachet in endosymbiotic bacteria. Proc Natl Acad Sci U S A, 1996. 93(7): p. 2873-8.
[30]     Liu SK, Eisen JA, Hanawalt PC, Tessman IW. 1993. recA mutations that reduce the constitutive coprotease activity of the RecA1202(PrtC) protein: possible involvement of interfilament association in proteolytic and recombination activities. J. Bacteriol. 175: 6518-6529.
[31]     Eisen JA. 1995. The RecA protein as a model molecule for molecular systematic studies of bacteria: comparison of trees of RecAs and 16S rRNAs from the same species. J. Mol. Evol. 41: 1105-1123.
[32]     Eisen JA, Sweder KS, Hanawalt PC. 1995. Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions. Nucl. Acids Res. 23: 2715-2723.
[33]     Eisen JA, Kaiser D, Myers RM. 1997. Gastrogenomic delights: a movable feast. Nature Medicine 3: 1076-1078.
[34]     Eisen JA. 1998. Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Res. 8: 163-167.
[35]     Eisen JA. 1998. A phylogenomic study of the MutS family of proteins. Nucl. Acids Res. 26: 4291-4300.
[36]     Eisen JA. Hanawalt PC. 1999. A phylogenomic study of DNA repair genes, proteins, and processes. Mut. Res. 435: 171-213.
[37]     Bjorkholm B, Sjolund M, Falk PG, Berg OG, Engstrand L, Andersson DI. 2001. Mutation frequency and biological cost of antibiotic resistance in Helicobacter pylori. Proc Natl Acad Sci U S A. 98(25):14607-12.
[38]     Britt AB, Eisen JA. 2000. DNA repair and recombination. In ‘Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.’Nature 408: 796-815.
[39]     Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, Carlton JM, Pain A, Nelson KE, Bowman S, Paulsen IT, James K, Eisen JA, Rutherford K, Salzberg SL, Craig A, Kyes S, Chan MS, Nene V, Shallom SJ, Suh B, Peterson J, Angiuoli S, Pertea M, Allen J, Selengut J, Haft D, Mather MW, Vaidya AB, Martin DM, Fairlamb AH, Fraunholz MJ, Roos DS, Ralph SA, McFadden GI, Cummings LM, Subramanian GM, Mungall C, Venter JC, Carucci DJ, Hoffman SL, Newbold C, Davis RW, Fraser CM, Barrell B. 2002. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419: 498-511.
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[43]     Fleischmann RD, Alland D, Eisen JA, Carpenter L, White O, Peterson J, DeBoy R, Dodson R, Gwinn M, Haft D, Hickey E, Kolonay JF, Nelson WC, Umayam LA, Ermolaeva M, Salzberg SL, Delcher A, Utterback T, Weidman J, Khouri H, Gill J, Mikula A, Bishai W, Jacobs WR Jr, Venter JC, Fraser CM. 2002. Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains. J. Bacteriol.184: 5479-5490.
[44]     Wood DW, Setubal JC, Kaul R, Monks DE, Kitajima JP, Okura VK, Zhou Y, Chen L, Wood GE, Almeida Jr. NF, Woo L, Chen Y, Paulsen IT, Eisen JA, Karp PD, Bovee Sr. D, Chapman P, Clendenning J, Deatherage G, Gillet W, Grant C, Kutyavin T, Levy R, Li M-J, McClelland R, Palmieri A, Raymond C, Rouse G, Saenphimmachak C, Wu Z, Romero P, Gordon D, Zhang S, Yoo H, Tao Y, Biddle P, Jung M, Krespan W, Perry M, Gordon-Kamm B, Liao L, Kim S, Hendrick C, Zhao Z-Y, Dolan M, Chumley F, Tingey SC, Tomb J-F, Gordon MP, Olson MV, Nester EW. 2001. The genome of the natural genetic engineer Agrobacterium tumefaciens C58. Science 294: 2317-2323.

EVE198 / EVE161 Microbial Phylogenomics Course Spring 2012


EVE 198 – Spring Quarter 2012 – CRN 74485 – 3 units P/NP grading

Microbial Phylogenomics:  The Evolutionary Diversification of Microbes and their Genomes

Professor Jonathan Eisen



TR 1:40-3:00pm

Room 1344 Storer Hall

 Prerequisites for this EVE 198 / Jonathan Eisen course are BIS 2ABC (or its equivalent, for transfer students). (This course is moving through the course approval process, and will eventually be EVE 161!)