Alm:Publications

DNA phosphorothioation is widespread and quantized in bacterial genomes.
Wang L, Chen S, Vergin KL, Giovannoni SJ, Chan SW, DeMott MS, Taghizadeh K, Cordero OX, Cutler M, Timberlake S, Alm EJ, Polz MF, Pinhassi J, Deng Z, Dedon PC.
Proc Natl Acad Sci U S A. 2011 Feb 15;108(7):2963-8. Epub 2011 Feb 1.
PMID: 21285367

Rapid evolutionary innovation during an Archaean genetic expansion.
David LA, Alm EJ.
Nature. 2011 Jan 6;469(7328):93-6. Epub 2010 Dec 19.
PMID: 21170026

Local gene regulation details a recognition code within the LacI transcriptional factor family.
Camas FM, Alm EJ, Poyatos JF.
PLoS Comput Biol. 2010 Nov 11;6(11):e1000989.
PMID: 21085639

Metapopulation structure of Vibrionaceae among coastal marine invertebrates.
Preheim SP, Boucher Y, Wildschutte H, David LA, Veneziano D, Alm EJ, Polz MF.
Environ Microbiol. 2011 Jan;13(1):265-75. doi: 10.1111/j.1462-2920.2010.02328.x. Epub 2010 Sep 1.
PMID: 20819104

Unlocking short read sequencing for metagenomics.
Rodrigue S, Materna AC, Timberlake SC, Blackburn MC, Malmstrom RR, Alm EJ, Chisholm SW.
PLoS One. 2010 Jul 28;5(7):e11840.
PMID: 20676378

Global transcriptional, physiological, and metabolite analyses of the responses of Desulfovibrio vulgaris hildenborough to salt adaptation.
He Z, Zhou A, Baidoo E, He Q, Joachimiak MP, Benke P, Phan R, Mukhopadhyay A, Hemme CL, Huang K, Alm EJ, Fields MW, Wall J, Stahl D, Hazen TC, Keasling JD, Arkin AP, Zhou J.
Appl Environ Microbiol. 2010 Mar;76(5):1574-86. Epub 2009 Dec 28.
PMID: 20038696

MicrobesOnline: an integrated portal for comparative and functional genomics.
Dehal PS, Joachimiak MP, Price MN, Bates JT, Baumohl JK, Chivian D, Friedland GD, Huang KH, Keller K, Novichkov PS, Dubchak IL, Alm EJ, Arkin AP.
Nucleic Acids Res. 2010 Jan;38(Database issue):D396-400. Epub 2009 Nov 11.
PMID: 19906701

Looking for Darwin's footprints in the microbial world.
Shapiro BJ, David LA, Friedman J, Alm EJ.
Trends Microbiol. 2009 May;17(5):196-204. Epub 2009 Apr 15. Review.
PMID: 19375326

Engineering transcription factors with novel DNA-binding specificity using comparative genomics.
Desai TA, Rodionov DA, Gelfand MS, Alm EJ, Rao CV.
Nucleic Acids Res. 2009 May;37(8):2493-503. Epub 2009 Mar 5.
PMID: 19264798

The bacterial species challenge: making sense of genetic and ecological diversity.
Fraser C, Alm EJ, Polz MF, Spratt BG, Hanage WP.
Science. 2009 Feb 6;323(5915):741-6. Review.
PMID: 19197054

Environmental genomics reveals a single-species ecosystem deep within Earth.
Chivian D, Brodie EL, Alm EJ, Culley DE, Dehal PS, DeSantis TZ, Gihring TM, Lapidus A, Lin LH, Lowry SR, Moser DP, Richardson PM, Southam G, Wanger G, Pratt LM, Andersen GL, Hazen TC, Brockman FJ, Arkin AP, Onstott TC.
Science. 2008 Oct 10;322(5899):275-8.
PMID: 18845759

• DNA from 2.8 km deep in the Earth’s crust reveals the genetic complement necessary for a single species ecosystem.

Resource partitioning and sympatric differentiation among closely related bacterioplankton.
Hunt DE, David LA, Gevers D, Preheim SP, Alm EJ, Polz MF.
Science. 2008 May 23;320(5879):1081-5.
PMID: 18497299

• Identifying ecologically differentiated populations within complex microbial communities remains challenging, yet is critical for interpreting the evolution and ecology of microbes in the wild. Here, we describe spatial and temporal resource partitioning among Vibrionaceae strains coexisting in coastal bacterioplankton. A quantitative model (AdaptML) establishes the evolutionary history of ecological differentiation, thus revealing populations specific for seasons and lifestyles (combinations of free-living, particle, or zooplankton associations). These ecological population boundaries frequently occur at deep phylogenetic levels (consistent with named species); however, recent and, perhaps, ongoing adaptive radiation is evident in Vibrio splendidus, which comprises numerous ecologically distinct populations at different levels of phylogenetic differentiation. Thus, environmental specialization may be an important correlate or even a trigger of speciation among sympatric microbes.

Shapiro BJ, Alm EJ (2008) Comparing Patterns of Natural Selection across Species Using Selective Signatures. PLoS Genetics 4(2): e23 doi:10.1371/journal.pgen.0040023 pmid: 18266472

• Comparing gene expression profiles over many different conditions has led to insights that were not obvious from single experiments. In the same way, comparing patterns of natural selection across a set of ecologically distinct species may extend what can be learned from individual genome-wide surveys. Toward this end, we show how variation in protein evolutionary rates, after correcting for genome-wide effects such as mutation rate and demographic factors, can be used to estimate the level and types of natural selection acting on genes across different species. We identify unusually rapidly and slowly evolving genes, relative to empirically derived genome-wide and gene family-specific background rates for 744 core protein families in 30 γ-proteobacterial species. We describe the pattern of fast or slow evolution across species as the “selective signature” of a gene. Selective signatures represent a profile of selection across species that is predictive of gene function: pairs of genes with correlated selective signatures are more likely to share the same cellular function, and genes in the same pathway can evolve in concert. For example, glycolysis and phenylalanine metabolism genes evolve rapidly in Idiomarina loihiensis, mirroring an ecological shift in carbon source from sugars to amino acids. In a broader context, our results suggest that the genomic landscape is organized into functional modules even at the level of natural selection, and thus it may be easier than expected to understand the complex evolutionary pressures on a cell.

Alm E, Huang K, Arkin A (2006) The evolution of two-component systems in bacteria reveals different strategies for niche adaptation. PLoS Comput Biol. 2006 Nov 3;2(11):e143

• Pathways containing histidine protein kinases (HPKs) represent a key mechanism for signal transduction, especially in bacteria. These systems help cells to sense and respond to their environment by detecting external cues and effecting internal responses such as changes in gene expression. As such, they are believed to play a key role in niche adaptation, yet their evolution is difficult to study due to the large number of paralogous subfamilies. This work extends previous large-scale gene evolution studies by considering complex paralogy relationships, and uncovers an abundance of horizontal transfers, gene duplications, and domain shuffling that have marked the evolutionary history of HPKs. An important finding of this study is qualitative differences between the main strategies for acquiring new HPKs (horizontal gene transfer and gene duplication). Hallmarks of the latter process include domain shuffling and the generation of “orphan” HPKs not co-transcribed with a cognate response regulator.

Price MN, Arkin AP, Alm EJ (2006) The life-cycle of operons. PLoS Genetics 2006 Jun;2(6):e96

• In bacteria, adjacent genes are often transcribed together in operons. Which genes are placed together in operons varies greatly across bacteria. This diversity of operon structure can be used to predict the function of genes: genes that are sometimes in an operon are likely to have related functions, even if they are transcribed separately in the organism of interest. However, it has not been clear why this diversity exists or what its consequences are. This work reconstructs evolutionarily recent changes to operon structures in the well-studied bacterium Escherichia coli. Changes in operon structure are shown to be associated with changes in gene expression patterns, so the diversity in operon structure may reflect adaptation to differing lifestyles. Indeed, some of these changes appear to be beneficial to the organism. This work also reconstructs the molecular mechanisms of operon evolution. Understanding these mechanisms should aid other analyses of bacterial genomes. For example, new operons often arise by deleting the DNA between functionally unrelated genes that happen to be near each other. Thus, recently evolved operons should not be used to infer their genes' function. Overall, this work provides a framework for understanding the evolutionary life-cycle of operons.