Introduction Atlas of Bacterial and Archaeal Cell Structure Home

Acknowledgments

We are grateful to Rob Phillips, our colleague at Caltech, for impressing Grant with the lasting value of Fawcett’s Atlas and encouraging him to create another. Readers of early drafts, including Lydia Jensen and Natalie Jensen, gave us useful feedback to improve this experience. We particularly thank Grigorios Oikonomou and past and present Jensen Lab members for advice and feedback. We are grateful to Ashley Jensen and Tony Kukavica for help with research. We are deeply grateful to Travis Alvarez, Camille Ogilvie, Natalie Jensen and Aditee Prabhutendolkar, who created most of the movies. And we are most grateful of all to our colleagues whose work at the microscope filled these pages. Click on their names throughout the book to learn a little bit more about them.

All of the images in this book were acquired in the course of research projects. Major funding for these projects in the Jensen Lab has come from the National Institutes of Health (NIH), Howard Hughes Medical Institute, Beckman Institute, Gordon and Betty Moore Foundation, Agouron Institute, and John Templeton Foundation. Cryo-electron microscopy was performed in the Beckman Institute Resource Center for Transmission Electron Microscopy at Caltech and the HHMI Janelia Farm CryoEM Facility. Most of these projects were also collaborative, and we thank the researchers who provided the cells we imaged, from the groups of Gladys Alexandre, Yannick Bomble, Sean Crosson, Mike Dyall-Smith, Moh El-Naggar, Robert Gunsalus, Alan Hauser, Chris Hayes, Bill Hickey, Matthias Horn, Jack Johnson, Marina Kalyuzhnaya, Arash Komeili, Jared Leadbetter, Eric Matson, Sarkis Mazmanian, John Mekalanos, Dianne Newman, Victoria Orphan, Tracy Palmer, Kit Pogliano, Eric Reynolds, Carrie Shaffer, Nicholas Shikuma, Liz Sockett, Lotte Sogaard-Andersen, David Stahl, Ronald Taylor, Martin Thanbichler, Kasthuri Venkateswaran, Joseph Vogel, Matthew Waldor, Kylie Watts, Douglas Weibel, and Patricia Zambryski.

We used the IMOD software package (developed by David Mastronarde, Rick Gaudette, Sue Held, Jim Kremer, Quanren Xiong, John Heumann and others at the University of Colorado with support from the NIH) to create and visualize tomographic datasets, and we are grateful to David Mastronarde for his tireless support of the software, including improving a function to help us make these movies. We used UCSF Chimera (developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco, with support from NIH grant P41 GM103311) to create the visualizations of atomic models from the Worldwide Protein Data Bank (wwPDB). We generated and visualized the phylogenetic tree with phyloT and iTOL [5]. We thank Lam Nguyen for generating the atomic model of a lipid bilayer, and Jane Ding, Andrew Jewett, Yi-Wei Chang, Ariane Briegel and Min Xu for 3D segmentations. High-resolution structures of proteins and complexes are the work of many labs; see references for full details. Likewise, our understanding of the functions of cellular structures derives from the enormous body of work of generations of scientists.

The Caltech Library, including Kristin Briney, Robert Doiel, Donna Wrublewski and Gail Clement, supported and enabled our vision of open access publishing and we are enormously grateful for their work and ingenuity in creating a platform tailored to the content and our shared vision of open accessibility. We are particularly grateful to Thomas Morrell for coordinating the technical infrastructure. We thank Vicki Chiu for design advice. Last but not least, we thank Kian Badie for creating the web interface.

Introduction

In the 1960s, electron microscopes were opening a new window in biology, allowing scientists to look not just at cells, but into them. This revealed a rich world of ultrastructures too small to resolve with light microscopes, including organelles inside eukaryotic cells. To share this new vista with scientists and medical students who did not have microscopes to look for themselves, authors like Don Fawcett [2] and John Dodge [3] created atlases of electron microscopy images that remain valuable resources for biological and medical novices, as well as experts.

More than fifty years later, we are once again enjoying an expanded view of biology, thanks to another great advance in electron microscopy. The development of cryogenic electron microscopy, or cryo-EM, allows us to look inside cells in their native state. This has opened up even the smallest cells for examination, and revealed some surprising things. In particular, bacteria and archaea, orders of magnitude smaller than eukaryotic cells and lacking prominent organelles, previously seemed to be relatively unstructured bags of nucleic acids and protein. In the last decade, cryo-EM has challenged this idea, revealing a startling degree of structure in these tiny cells. Understanding this intricate molecular machinery might enable us to engineer new biological tools in the future. And so, inspired by the atlases of eukaryotic cell structure from the 1960s, here we offer an atlas of bacterial and archaeal cell structure, highlighting many of the molecular machines we have discovered so far. We hope it will be a useful tool for microbiology courses, serving as a quick introduction to the cells and what they contain before students go on to study aspects of biochemistry or medical importance.

Just as the technology of electron microscopy has advanced in the intervening decades, the technology of sharing information has similarly evolved. Taking advantage of a digital medium, we can share not just two-dimensional slices through cells, but full three-dimensional volumes with movies and animations. This medium also allows you to tailor your experience. If you want a brief overview, simply follow the main narrative. If you want to go into more depth on a topic, use the “Learn More” buttons to see additional examples and details. If you are interested in a particular species, navigate from the Phylogenetic Tree. If you are interested in a particular structure, try out the Feature Index. The digital format also lends itself to frequent updates so the textbook can better reflect an active field of research. To see what has been added in each new edition, check out About this Book.

If you are new to cryo-EM, we suggest starting with Chapter 1, which describes the methods used in structural biology, particularly cryo-EM. If you are already an expert, or pressed for time, go straight to the cells in Chapter 2. Before you do, though, please watch this short introductory video.

As Charles Darwin wrote in 1837, “I shall always feel respect for every one who has written a book, let it be what it may, for I had no idea of the trouble which trying to write common English could cost one” [4]. The task was made immeasurably easier for us by the help of many minds and hands. See acknowledgments below ⇩.

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