COMMENTARY COMMENTARY Insights into the life of an oxygenic phototroph William B. Whitman1 The fourth and most challenging task will be Department of Microbiology, University of Georgia, Athens, GA 30602 linking the wealth of phylogenetic and geno- mic information to the properties of the living organisms. The paper by Rubin et al. (1) con- We have the capability of completing the first among us. This description is an enormous tributes to this important goal for the oxygenic draft of the description of life on Earth within challenge and will be one of the great accom- phototroph elongatus PCC7942. the lifetime of many of the youngest scientists plishments of modern science. It will yield In this work, Rubin et al. use a combina- fundamental paradigm shifts in biology and tion of high-density transposon mutagenesis revolutionary breakthroughs in medicine, and next-generation sequencing called TnSeq agriculture, and biotechnology. Like life, a to evaluate the contribution of each gene to meaningful description of life will be enor- fitness during growth under laboratory con- mously complex. Although it will certainly ditions (1). These experiments provide a comprise grand generalizations and natural wealth of information about gene function, laws, it will also include sufficient detail to but they are especially challenging because capture the nuances of life and unite molec- they require very high rates of genetic trans- ular biology with natural history. The PNAS formation. In fact, of the 34 experiments of paper by Rubin et al. (1) is a major step to- this type performed on prokaryotes listed in a ward this goal by providing a detailed exam- recent database, only 6 were performed on ination of gene function in a cyanobacterium, environmentally important organisms (11). one of the dominant groups of oxygenic pho- This fact reflects the difficulty of manipu- tosynthetic organisms on Earth. lating many of these largely understudied This modern description of life will have and mysterious organisms. Despite their four components. The first will be a complete abundance and major roles in biogeochem- censusofthemajoreukaryoticandpro- ical cycles, only a minute fraction have karyotic lineages on Earth. Depending upon yielded to laboratory investigation. As a con- how major is defined, the census of macro- sequence, little is known about their most biota might be considered largely complete basic biological properties. (2). Even for microorganisms, rapid progress To my knowledge, Synechococcus elongatus is being made. For instance, it is likely that PCC7942 is the first cyanobacterium and first most of the diversity of the 16S rRNA genes phototroph interrogated by this technique. representing the major lineages of prokary- Because it is an obligate photolithotroph, otes will have been discovered by the end of these experiments yield insights into photo- this decade (3). The second component will synthesis and autotrophic CO assimilation be sampling of sequences of repre- 2 that have been previously unavailable. Of par- sentatives of each of the major lineages. Al- ticular value was the ability to test the essen- though this task remains daunting, especially tiality of all of the components of the for the single-celled eukaryotes, rapid prog- photosystems and associated electron trans- ress is being made among the prokaryotes. port chains, providing a rigorous test of the Noteworthy are the efforts to sequence ge- state of our knowledge about these complex, nomes of all of the named prokaryotes (4) multiprotein systems. Similarly, the pathways as well representatives of the very diverse of central metabolism that convey carbon and uncultured lineages often called “micro- Fig. 1. Morphology of Synechococcus elongatus from CO through the reductive pentose bial dark matter” (5–7). The third compo- 2 PCC7942. (A) Cells are short rods about 1.5 μmindiameter phosphate pathway into amino acids and that divide by binary fission. Although nonmotile, they pos- nent will be developing an understanding other biosynthetic precursors are of special sess numerous pili of unknown function. (Scale bar: 0.5 μm.) of the evolutionary processes that have and Cells and pili were visualized in this transmission electron will continue to occur within living organisms, interest in these autotrophs. Here, the exper- micrograph of intact cells by negative staining with uranyl especially the prokaryotes and single-celled iments of Rubin et al. reveal an unknown acetate by Timo Meerloo (Electron Microscopy Facility, Uni- flexibility and ability to dispense with a major versity of California at San Diego, La Jolla, CA). (B)Thecell eukaryotes (8, 9). In addition to revealing interior is packed with concentric membranes that the history of life on Earth, this understand- are the site of photosynthesis. (Scale bar: 0.5 μm.) Cells were ing will allow us to infer the properties of Author contributions: W.B.W. wrote the paper. embedded in resin and ultrathin sectioned by Ying Jones The author declares no conflict of interest. (Electron Microscopy Facility, University of California at San organisms based upon those of their relatives Diego, La Jolla, CA). Samples and images courtesy of Ryan (10). The availability of genome sequences See companion article 10.1073/pnas.1519220112. Simkovsky (University of California at San Diego, La Jolla, CA). will be key to understanding these processes. 1Email: [email protected].

www.pnas.org/cgi/doi/10.1073/pnas.1520098112 PNAS Early Edition | 1of2 Downloaded by guest on September 28, 2021 segment of the tricarboxylic acid cycle. As waters. Although not the most abundant cya- metabolism, responses to iron and other nu- important, these experiments open new areas nobacterial phototrophs in most marine wa- trient stresses, adaptations to temperature of investigation into regulation by noncoding ters, they still represent one of the most and light intensity, and circadian clock have RNAs. The dataset generated is extensive, abundant microorganisms on Earth (12). Al- also been extensively studied. With methods and more than 246,000 mutations were though S. elongatus PCC7942 is a freshwater to conveniently transfer in DNA being read- mapped onto the 2.80-Mbp genome. Thus, and not closely related to the marine ily available, it is also a platform for metabolic it will be the starting point for many addi- strains, it shares enough properties with them engineering production of commodity chem- tional studies of gene function and a valuable to serve as a good model for their basic bi- icals (14) and host for a commercially avail- resource for many laboratories with different ology (13). Moreover, its carbon and nitrogen ableproteinexpressionkit. interests in . Synechococcus elongatus PCC7942 was a good choice for these experiments. A unicel- 1 Rubin BE, et al. (2015) The essential gene set of a photosynthetic 9 Hinchliff CE, et al. (2015) Synthesis of phylogeny and organism. Proc Natl Acad Sci USA, 10.1073/pnas.1519220112. into a comprehensive tree of life. Proc Natl Acad Sci USA 112(41): lular cyanobacterium, it possesses many fea- 2 Mora C, Tittensor DP, Adl S, Simpson AG, Worm B (2011) How 12764–12769. tures typical of this group, including the many species are there on Earth and in the ocean? PLoS Biol 9(8): 10 Langille MGI, et al. (2013) Predictive functional profiling of complex intracytoplasmic membranes called e1001127. microbial communities using 16S rRNA marker gene sequences. Nat 3 Yarza P, et al. (2014) Uniting the classification of cultured and Biotechnol 31(9):814–821. that are the site of photosynthesis uncultured and archaea using 16S rRNA gene sequences. 11 Luo H, Lin Y, Gao F, Zhang CT, Zhang R (2014) DEG 10, an (Fig. 1) and carboxysomes, an inclusion body Nat Rev Microbiol 12(9):635–645. update of the database of essential genes that includes both protein- formed largely of a paracrystalline array of 4 Kyrpides NC, et al. (2014) Genomic encyclopedia of bacteria and coding genes and noncoding genomic elements. Nucleic Acids Res archaea: Sequencing a myriad of type strains. PLoS Biol 12(8): 42(Database issue):D574–D580. the key enzyme of the reductive pentose phos- e1001920. 12 Scanlan DJ, West NJ (2002) Molecular ecology of the marine phate pathway RuBisCO. Moreover, they 5 Rinke C, et al. (2013) Insights into the phylogeny and coding cyanobacterial genera Prochlorococcus and Synechococcus. FEMS potential of microbial dark matter. Nature 499(7459):431–437. Microbiol Ecol 40(1):1–12. share features with many heterotrophic bac- 6 Spang A, et al. (2015) Complex archaea that bridge the gap 13 Herdman M, et al. (2001) Form-genus XIII. Synechococcus. teria, such as a complex cell wall structure and between prokaryotes and eukaryotes. Nature 521(7551):173–179. Bergey’s Manual of Systematic Bacteriology, eds Boone DR, cellular appendages composed of the protein 7 Brown CT, et al. (2015) Unusual biology across a group comprising Castenholz RW (Springer, New York), Vol 1, pp 508–512. more than 15% of domain Bacteria. Nature 523(7559):208–211. 14 Angermayr SA, Gorchs Rovira A, Hellingwerf KJ (2015) Metabolic pilin. Species of the genus Synechococcus are 8 Doolittle WF (2015) Rethinking the tree of life. Microbe 10(8): engineering of cyanobacteria for the synthesis of commodity common in fresh as well as marine surface 319–323. products. Trends Biotechnol 33(6):352–361.

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