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Mol Biol Cell. Apr 15, 2013; 24(8): 1099–1102.
PMCID: PMC3623631
Tiny cells meet big questions: a closer look at bacterial cell biology
Erin D. Goley1
Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205
David G. Drubin, Monitoring Editor
University of California, Berkeley
1Address correspondence to: Erin D. Goley (egoley1/at/jhmi.edu).
Received December 31, 2012; Revised February 12, 2013; Accepted February 14, 2013.
While studying actin assembly as a graduate student with Matt Welch at the University of California at Berkeley, my interest was piqued by reports of surprising observations in bacteria: the identification of numerous cytoskeletal proteins, actin homologues fulfilling spindle-like functions, and even the presence of membrane-bound organelles. Curiosity about these phenomena drew me to Lucy Shapiro's lab at Stanford University for my postdoctoral research. In the Shapiro lab, and now in my lab at Johns Hopkins, I have focused on investigating the mechanisms of bacterial cytokinesis. Spending time as both a eukaryotic cell biologist and a bacterial cell biologist has convinced me that bacterial cells present the same questions as eukaryotic cells: How are chromosomes organized and accurately segregated? How is force generated for cytokinesis? How is polarity established? How are signals transduced within and between cells? These problems are conceptually similar between eukaryotes and bacteria, although their solutions can differ significantly in specifics. In this Perspective, I provide a broad view of cell biological phenomena in bacteria, the technical challenges facing those of us who peer into bacterial cells, and areas of common ground as research in eukaryotic and bacterial cell biology moves forward.
By now, it is widely recognized that a description of bacteria as “bags of enzymes” that lack dedicated mechanisms of spatial order is inaccurate and obsolete. Early indications that some bacterial species might possess mechanisms of spatial organization came from simply observing cell morphology: sporulating organisms like Bacillus subtilis develop a forespore at one end of the cell and not the other; dimorphic species like Caulobacter crescentus exhibit distinct polar appendages at different stages of the cell cycle; more broadly, bacteria can adopt a variety of cell shapes that result from polarized growth (Young, 2006 blue right-pointing triangle). Each of these examples suggests an underlying architecture to spatially restrict growth, signaling, or development. Indeed, with the advent of green fluorescent protein (GFP) fusion technology in the mid-1990s, many bacterial proteins were demonstrated to localize within the cell, often dynamically so in response to cell cycle or developmental cues. Some of the earliest studies with GFP fusion proteins illustrated dynamic localization of sporulation factors (Webb et al., 1995 blue right-pointing triangle), cell cycle regulators (Jacobs et al., 1999 blue right-pointing triangle), and cell division proteins (Ma et al., 1996 blue right-pointing triangle). Since then, hundreds of bacterial proteins have been localized, and a recent whole-genome view of protein localization in C. crescentus indicates that >10% of proteins have a particular address within the cell (Werner et al., 2009 blue right-pointing triangle). Beyond proteins, the bacterial chromosome is highly ordered in space (Reyes-Lamothe et al., 2012 blue right-pointing triangle), mRNAs can be localized (Montero Llopis et al., 2010 blue right-pointing triangle), lipid microdomains have been observed (Mileykovskaya and Dowhan, 2000 blue right-pointing triangle), and small signaling molecules can show asymmetric distribution (Christen et al., 2010 blue right-pointing triangle). Precise spatial distribution of proteins and other cellular components appears to be a universal feature of bacteria, even those that lack obvious asymmetry.
Perhaps it is not so surprising that bacteria localize their proteins and other biomolecules. More startling are discoveries that defy conventional definitions of “eukaryote” and “prokaryote.” For example, I was taught in undergraduate cell biology that endomembrane systems were a defining characteristic of eukaryotic cells. Although it is certainly true that bacteria do not possess the stereotypical organelles of eukaryotes, there are organisms that come surprisingly close. These bacterial species elaborate extensions of their cytoplasmic membranes to create specialized compartments or even form structurally independent membrane-bound organelles. The magnetosomes of Magnetospirillum magneticum (Komeili et al., 2006 blue right-pointing triangle), photosynthetic membranes of several classes of bacteria (Murat et al., 2010 blue right-pointing triangle), and nuclear envelope (Fuerst and Webb, 1991 blue right-pointing triangle) and endocytosis events (Lonhienne et al., 2010 blue right-pointing triangle) in planctomycetes like Gemmata obscuriglobus are emerging as models for understanding bacterial endomembranes. A focus on the cell biology of these compartments is fairly recent, and there are more questions than answers. How are internal membranes shaped in bacteria? How are they duplicated and segregated as the cell grows and divides? How are proteins and other molecules targeted to and retained in these compartments? Answering these questions may provide insight into the origins of eukaryotic organelles and allow engineering or manipulation of compartments for synthetic biology applications.
A second example of a canonically eukaryotic element popping up in bacteria, and the one that first drew my attention to bacterial cell biology, was the discovery of bacterial cytoskeletal proteins. FtsZ was the first such protein described: in the early 1990s it was shown to be a polymerizing GTPase that localizes to the cell division site (Erickson, 1995 blue right-pointing triangle), and in 1998 it was confirmed as a tubulin homologue when high-resolution structures of each revealed the remarkable similarity of their folds (Löwe and Amos, 1998 blue right-pointing triangle; Nogales et al., 1998 blue right-pointing triangle). Since then, the list of bacterial cytoskeletal proteins has expanded to include dozens of families of actin homologues, at least four families of tubulin homologues, intermediate filament–like proteins, CTP synthase, and bacterial-specific, polymer-forming proteins like Walker A cytoskeletal ATPases and bactofilins (Ingerson-Mahar and Gitai, 2012 blue right-pointing triangle). Bacterial cytoskeletal proteins fulfill cellular roles analogous to their eukaryotic counterparts: segregating genetic material, directing polarity and growth, orchestrating cytokinesis, organizing membranes, and scaffolding protein complexes. We are making significant strides in the biochemical and structural characterization of these factors, but progress in understanding their regulation and mechanisms of action in the cell has been slower. Do FtsZ and the actin homologue MreB generate force to direct cell wall remodeling during division and growth or simply serve as scaffolds for the protein complexes that do the heavy lifting? What polymeric species are present in the cell, and how do polymer structures relate to their function? The bacterial cytoskeleton has drawn substantial interest from eukaryotic cell biologists, as findings about the behavior, structure, and regulation of bacterial actins and tubulins may be relevant to their eukaryotic homologues and may establish unifying principles of cytoskeletal function (Löwe and Amos, 2009 blue right-pointing triangle).
Bacterial species encompass enormous diversity, so I cannot begin to enumerate all of the cell biological questions they present. In the foregoing I described two areas that are surprisingly reminiscent of canonical eukaryotic cell biology. In looking through the program from the latest ASCB Annual Meeting, I can think of bacterial cell biological processes that could fall readily under most of the headings for Symposia, Minisymposia, and Poster Sessions. Table 1 provides examples of parallels to major areas of eukaryotic cell biological research and directs the reader to reviews on these topics.
TABLE 1:
TABLE 1:
Bacterial parallels to eukaryotic cell biological phenomena and examples of the model systems used to study them.
My move from studying actin regulation in eukaryotic systems to studying FtsZ function in a bacterium revealed advantages, and challenges, to working on bacterial cell biology. An obvious disadvantage is the fact that most bacteria are on the same size scale as eukaryotic organelles, making imaging subcellular structures a challenge. When the diameter of your cell is only twice the resolution limit of a light microscope, every incremental increase in resolution counts. With superresolution imaging techniques the picture we obtain of the bacterial cytokinetic ring in living cells, for example, is vastly improved over widefield fluorescence microscopy (Fu et al., 2010 blue right-pointing triangle; Biteen et al., 2012 blue right-pointing triangle; Strauss et al., 2012 blue right-pointing triangle), but it is not yet to the point that we can resolve the individual FtsZ filament structures within it. Electron cryotomography (ECT) allows for beautiful visualization of cytoskeletal filaments, membranes, and other macromolecular structures at high resolution in cryopreserved cells (Li and Jensen, 2009 blue right-pointing triangle). ECT relies on natural contrast in the sample, however, and is not yet compatible with protein-labeling strategies, so the picture it presents may not be comprehensive. Bacterial cell biologists are poised to benefit in a big way from continued technical advances in superresolution, single-molecule, and ECT approaches. We would also benefit from the development of tools that allow us to specifically and rapidly dissect cell biological phenomena. I sorely miss the array of well-characterized small-molecule inhibitors and probes of cytoskeletal, trafficking, or other events available for eukaryotic cells. Here, again, it is a matter of time, as continued effort is being invested in developing the tools we need to characterize cell biological events in bacteria.
Along with the downsides, there are the tremendous advantages to working in bacteria: they have comparatively small genomes, short reproduction times, and, in many cases, well-developed genetic and genomic tools. Thus it is fairly fast and straightforward to address the function of a gene of interest in vivo or take a systems-level view of a particular phenomenon. The relatively small parts list of bacterial cells makes it feasible to address fundamental cell biological questions comprehensively (e.g., Skerker et al., 2005 blue right-pointing triangle; McKenney et al., 2010 blue right-pointing triangle; Goley et al., 2011 blue right-pointing triangle), reconstitute them in vitro (e.g., Garner et al., 2007 blue right-pointing triangle; Loose et al., 2008 blue right-pointing triangle), and model them in silico (e.g., Huang et al., 2003 blue right-pointing triangle; Shen et al., 2008 blue right-pointing triangle). Bacteria also offer tremendous ecological, morphological, and phylogenetic diversity that can be harnessed to select the ideal model system for a question of interest. For example, progress in understanding the structural basis of bacterial cytoskeletal function has been rapid in many cases, in part owing to the ability to use homologues from thermophilic bacteria for crystallographic studies. Moreover, as in eukaryotes, the ability to address the same cellular process in phylogenetically distant organisms allows one to discern universalities and variations in the execution and regulation of an event of interest. This approach has revealed that bacteria, perhaps more often than eukaryotes, can evolve distinct mechanisms for controlling the same fundamental process. A mitotic spindle-like chromosome segregation system (ParABS) exists in organisms like C. crescentus, Vibrio cholerae, and sporulating B. subtilis, for example, each of which exhibits clear cell polarity and targets its origin of replication to the cell pole. No such dedicated machinery has been identified in the morphologically symmetric organism Escherichia coli, which localizes its origin of replication near midcell (Reyes-Lamothe et al., 2012 blue right-pointing triangle). These differences highlight the inventiveness and efficiency of bacterial cells in optimizing their cell biology to their lifestyle and suggest that we might capitalize on these molecular distinctions to develop antibiotics that are specific to a subset of bacteria. Finally, what drew me to the field of bacterial cell biology is the fact that it is in its infancy and is laden with exciting, fundamental questions. Not only do we have work to do in uncovering the mechanistic basis of cell biological events and the nuances of their regulation in diverse species, but in addition there are undoubtedly phenomena that remain to be described and, even in well-studied processes like cytokinesis or chromosome organization, basic mechanisms to be elucidated.
So why should a eukaryotic cell biologist care about what is going on in bacterial cells? When it comes down to it, eukaryotic and bacterial cells are made of the same biomolecules, obey the same rules of chemistry and physics, and, therefore, often come up with similar strategies for accomplishing the same goal. In learning about a new phenomenon in bacteria, I am often struck by similarity to a cell biological process in eukaryotes and vice versa. Recently a diffusion barrier was described that limits entry of periplasmic and membrane proteins to the polar stalk of C. crescentus (Schlimpert et al., 2012 blue right-pointing triangle). This discovery immediately made me think of the diffusion barriers at the base of primary cilia (Hu and Nelson, 2011 blue right-pointing triangle). Although the molecules doing the job are different, the biophysical basis and functions of these barriers may be the same. Similarly, bacterial cells face challenges similar to those of fungal or plant cells during cytokinesis: each requires coordination of membrane ingression with cell wall remodeling in the face of high internal turgor pressure. Understanding how one of these systems works illuminates potential mechanisms in the others. From a practical perspective, new technologies for imaging, automated image and data analysis, or high-throughput studies advanced by bacterial cell biologists will benefit eukaryotic cell biologists and vice versa.
Research in bacterial cell biology is motivated by a variety of factors, ranging from the applied (e.g., identifying and characterizing targets for antibiotics) to the fundamental (e.g., elucidating basic biophysical or biochemical mechanisms behind polarity establishment or chromosome organization). With growing awareness of the microbiome, growing interest in synthetic biology, and growing resistance of bacterial pathogens to existing antibiotics, the practical benefits of a detailed knowledge of bacterial cells continue to expand. Bacterial cell biologists are using all of the tools of modern biology—genetics, genomics, microscopy, biochemistry, systems biology, biophysics, and so on—to uncover the mechanisms and meaning of cell biological phenomena. Through this Perspective, I hope to have convinced eukaryotic cell biologists that it is worth their time to check out that talk on bacterial development or signaling or cytokinesis when they see it on the seminar schedule or in the ASCB Annual Meeting program. Likewise, I urge bacterial cell biologists to attend ASCB meetings and other conferences traditionally aimed at eukaryotic cell biologists. Once they get past the obvious differences, they may just find familiarity and inspiration.
Acknowledgments
I thank Seth Margolis, Elizabeth Meier, Monica Schwartz, and Jie Xiao for critical reading of the manuscript. I am grateful to my mentors, friends, and colleagues in both eukaryotic and bacterial cell biology for ideas and inspiration.
Abbreviations used:
ECTelectron cryotomography
GFPgreen fluorescent protein

  • Aguilar C, Vlamakis H, Losick R, Kolter R. Thinking about Bacillus subtilis as a multicellular organism. Curr Opin Microbiol. 2007;10:638–643. [PMC free article] [PubMed]
  • Biteen JS, Goley ED, Shapiro L, Moerner WE. Three-dimensional super-resolution imaging of the midplane protein FtsZ in live Caulobacter crescentus cells using astigmatism. Chemphyschem. 2012;13:1007–1012. [PubMed]
  • Christen M, Kulasekara HD, Christen B, Kulasekara BR, Hoffman LR, Miller SI. Asymmetrical distribution of the second messenger c-di-GMP upon bacterial cell division. Science. 2010;328:1295–1297. [PubMed]
  • Curtis PD, Brun YV. Getting in the loop: regulation of development in Caulobacter crescentus. Microbiol. Mol Biol Rev. 2010;74:13–41. [PMC free article] [PubMed]
  • Dworkin J. Cellular polarity in prokaryotic organisms. Cold Spring Harb Perspect Biol. 2009;1:a003368. [PMC free article] [PubMed]
  • Erickson HP. FtsZ, a prokaryotic homolog of tubulin. Cell. 1995;80:367–370. [PubMed]
  • Fu G, Huang T, Buss J, Coltharp C, Hensel Z, Xiao J. In vivo structure of the E. coli FtsZ-ring revealed by photoactivated localization microscopy (PALM) PLoS One. 2010;5:e12682. [PMC free article] [PubMed]
  • Fuerst JA, Sagulenko E. Beyond the bacterium: planctomycetes challenge our concepts of microbial structure and function. Nat Rev Microbiol. 2011;9:403–413. [PubMed]
  • Fuerst JA, Webb RI. Membrane-bound nucleoid in the eubacterium Gemmata obscuriglobus. Proc Natl Acad Sci USA. 1991;88:8184-8188. [PubMed]
  • Garner EC, Campbell CS, Weibel DB, Mullins RD. Reconstitution of DNA segregation driven by assembly of a prokaryotic actin homolog. Science. 2007;315:1270–1274. [PMC free article] [PubMed]
  • Goley ED, Yeh Y-C, Hong S-H, Fero MJ, Abeliuk E, McAdams HH, Shapiro L. Assembly of the Caulobacter cell division machine. Mol Microbiol. 2011;80:1680–1698. [PubMed]
  • Haeusser DP, Levin PA. The great divide: coordinating cell cycle events during bacterial growth and division. Curr Opin Microbiol. 2008;11:94–99. [PMC free article] [PubMed]
  • Hu Q, Nelson WJ. Ciliary diffusion barrier: the gatekeeper for the primary cilium compartment. Cytoskeleton (Hoboken) 2011;68:313–324. [PMC free article] [PubMed]
  • Huang KC, Meir Y, Wingreen NS. Dynamic structures in Escherichia coli: spontaneous formation of MinE rings and MinD polar zones. Proc Natl Acad Sci USA. 2003;100:12724–12728. [PubMed]
  • Ingerson-Mahar M, Gitai Z. A growing family: the expanding universe of the bacterial cytoskeleton. FEMS Microbiol Rev. 2012;36:256–267. [PubMed]
  • Jacobs C, Domian IJ, Maddock JR, Shapiro L. Cell cycle-dependent polar localization of an essential bacterial histidine kinase that controls DNA replication and cell division. Cell. 1999;97:111–120. [PubMed]
  • Komeili A, Li Z, Newman DK, Jensen GJ. Magnetosomes are cell membrane invaginations organized by the actin-like protein MamK. Science. 2006;13:242–245. [PubMed]
  • Li Z, Jensen GJ. Electron cryotomography: a new view into microbial ultrastructure. Curr Opin Microbiol. 2009;12:333–340. [PMC free article] [PubMed]
  • Lonhienne TG, Sagulenko E, Webb RI, Franke J, Devos DP, Nouwens A, Carroll BJ, Fuerst JA. Endocytosis-like protein uptake in the bacterium Gemmata obscuriglobus. Proc Natl Acad Sci USA. 2010;107:12883–12888. [PubMed]
  • Loose M, Fischer-Friedrich E, Ries J, Kruse K, Schwille P. Spatial regulators for bacterial cell division self-organize into surface waves in vitro. Science. 2008;320:789–792. [PubMed]
  • Löwe J, Amos LA. Crystal structure of the bacterial cell-division protein FtsZ. Nature. 1998;391:203–206. [PubMed]
  • Löwe J, Amos LA. Evolution of cytomotive filaments: the cytoskeleton from prokaryotes to eukaryotes. Int J Biochem Cell Biol. 2009;41:323–329. [PubMed]
  • Ma X, Ehrhardt DW, Margolin W. Colocalization of cell division proteins FtsZ and FtsA to cytoskeletal structures in living Escherichia coli cells by using green fluorescent protein. Proc Natl Acad Sci USA. 1996;93:12998–13003. [PubMed]
  • McKenney PT, Driks A, Eichenberger P. The Bacillus subtilis endospore: assembly and functions of the multilayered coat. Nat Rev Microbiol. 2012;11:33–44. [PubMed]
  • McKenney PT, Driks A, Eskandarian HA, Grabowski P, Guberman J, Wang KH, Gitai Z, Eichenberger P. A distance-weighted interaction map reveals a previously uncharacterized layer of the Bacillus subtilis spore coat. Curr Biol. 2010;20:934–938. [PMC free article] [PubMed]
  • Mileykovskaya E, Dowhan W. Visualization of phospholipid domains in Escherichia coli by using the cardiolipin-specific fluorescent dye 10-N-nonyl acridine orange. J Bacteriol. 2000;182:1172–1175. [PMC free article] [PubMed]
  • Montero Llopis P, Jackson AF, Sliusarenko O, Surovtsev I, Heinritz J, Emonet T, Jacobs-Wagner C. Spatial organization of the flow of genetic information in bacteria. Nature. 2010;466:77–81. [PMC free article] [PubMed]
  • Murat D, Byrne M, Komeili A. Cell biology of prokaryotic organelles. Cold Spring Harb Perspect Biol. 2010;2:a000422. [PMC free article] [PubMed]
  • Ng W-L, Bassler BL. Bacterial quorum-sensing network architectures. Annu Rev Gen. 2009;43:197–222. [PubMed]
  • Nogales E, Wolf SG, Downing KH. Structure of the alpha beta tubulin dimer by electron crystallography. Nature. 1998;391:199–203. [PubMed]
  • Patrick JE, Kearns DB. Swarming motility and the control of master regulators of flagellar biosynthesis. Mol Microbiol. 2012;83:14–23. [PMC free article] [PubMed]
  • Reyes-Lamothe R, Nicolas E, Sherratt DJ. Chromosome replication and segregation in bacteria. Annu Rev Genet. 2012;46:121–143. [PubMed]
  • Schlimpert S, et al. General protein diffusion barriers create compartments within bacterial cells. Cell. 2012;151:1270–1282. [PMC free article] [PubMed]
  • Shen X, Collier J, Dill D, Shapiro L, Horowitz M, McAdams HH. Architecture and inherent robustness of a bacterial cell-cycle control system. Proc Natl Acad Sci USA. 2008;105:11340–11345. [PubMed]
  • Skerker JM, Prasol MS, Perchuk BS, Biondi EG, Laub MT. Two-component signal transduction pathways regulating growth and cell cycle progression in a bacterium: a system-level analysis. PLoS Biol. 2005;3:e334. [PMC free article] [PubMed]
  • Strauss MP, Liew ATF, Turnbull L, Whitchurch CB, Monahan LG, Harry EJ. 3D-SIM super resolution microscopy reveals a bead-like arrangement for FtsZ and the division machinery: implications for triggering cytokinesis. PLoS Biol. 2012;10:e1001389. [PMC free article] [PubMed]
  • Typas A, Banzhaf M, Gross CA, Vollmer W. From the regulation of peptidoglycan synthesis to bacterial growth and morphology. Nat Rev Microbiol. 2012;10:123–136. [PubMed]
  • Webb CD, Decatur A, Teleman A, Losick R. Use of green fluorescent protein for visualization of cell-specific gene expression and subcellular protein localization during sporulation in Bacillus subtilis. J Bacteriol. 1995;177:5906–5911. [PMC free article] [PubMed]
  • Werner JN, Chen EY, Guberman JM, Zippilli AR, Irgon JJ, Gitai Z. Quantitative genome-scale analysis of protein localization in an asymmetric bacterium. Proc Natl Acad Sci USA. 2009;106:7858–7863. [PubMed]
  • Wickstead B, Gull K. Evolution: the evolution of the cytoskeleton. J Cell Biol. 2011;194:513–525. [PMC free article] [PubMed]
  • Young KD. The selective value of bacterial shape. Microbiol Mol Biol Rev. 2006;70:660–703. [PMC free article] [PubMed]
  • Young KD. Bacterial shape: two-dimensional questions and possibilities. Annu Rev Microbiol. 2010;64:223–240. [PMC free article] [PubMed]
  • Zhang Y, Ducret A, Shaevitz J, Mignot T. From individual cell motility to collective behaviors: insights from a prokaryote, Myxococcus xanthus. FEMS Microbiol Rev. 2012;36:149–164. [PubMed]
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