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60-473: C. crescentus C. daechungensis C. flavus C. fusiformis C. ginsengisoli C. heinricii C. hibisci C. mirabilis C. mirare C. profundis C. radicis C. rhizosphaerae C. segnis C. zeae Caulobacter is a genus of Gram-negative bacteria in the class Alphaproteobacteria . Its best-known member is Caulobacter crescentus , an organism ubiquitous in freshwater lakes and rivers; many members of

120-511: A Boron atom, and produced one of two new antifungal agents to be created in the last 25 years., approved by the FDA as a treatment for toe nail fungus, Kerydin. A second drug, Crisaborole, was developed to treat atopic dermatitis. In 2015, Shapiro, Benkovic, Fink and Schimmel founded Boragen, LLC to use the boron containing library for crop protection. Shapiro has advised both the Clinton administration and

180-414: A cell cycle protein. Yale University's data strongly suggest a model in which TipN regulates the orientation of the polarity axis by providing a positional cue from the preceding cell cycle. In this model TipN specifies the site of the most recent division by identifying the new pole. The cell uses this positional information as a source of intracellular asymmetry to establish and maintain the orientation of

240-524: A polarly localized protein in Caulobacter crescentus, has been shown to manipulate stalk positioning in these Asticcacaulis species. Presumably, It does so by a gain of function after protein expansion from around 400 amino acids in Caulobacter crescentus to more than 800 amino acids in Asticcacaulis species. Caulobacter was the first asymmetric bacterium shown to age. Reproductive senescence

300-409: A population even when they all are growing in identical environmental conditions. Cell cycle regulation includes feedback signals that pace progression of the cell cycle engine to match progress of events at the regulatory subsystem level in each particular cell. This control system organization, with a controller (the cell cycle engine) driving a complex system, with modulation by feedback signals from

360-434: A result of over-use of antibiotics since the 1950s. Shapiro is involved in development of drugs that will attack both a particular bacteria and its mechanisms of drug resistance, to prevent drug-resistant strains from developing. Another concern is the introduction of bacteria into previously unexposed populations, due to increased travel, population expansion into previously unexplored areas, and climate change . This includes

420-415: A state machine leads to understanding of bacterial cell cycle regulation as a whole cell phenomenon. In 2002, Shapiro founded Anacor Pharmaceuticals with physicist and developmental biologist Harley McAdams and chemist Stephen Benkovic of Pennsylvania State University . to design and develop new types of antibiotics and antifungals . They have developed a novel class of small molecules involving

480-426: Is a Gram-negative , oligotrophic bacterium widely distributed in fresh water lakes and streams. The taxon is more properly known as Caulobacter vibrioides (Henrici and Johnson 1935). C. crescentus is an important model organism for studying the regulation of the cell cycle , asymmetric cell division , and cellular differentiation . Caulobacter daughter cells have two very different forms. One daughter

540-415: Is a member of a group of bacteria that possess the stalk structure, a tubular extension from the cell body. However, the positioning of the stalk is not necessarily conserved at the pole of the cell body in different closely related species. Specifically, research has shown that not only the position of the stalk can change, but the number can vary as well in the closely related genus Asticcacaulis . SpmX,

600-467: Is a mobile "swarmer" cell that has a single flagellum at one cell pole that provides swimming motility for chemotaxis . The other daughter, called the "stalked" cell, has a tubular stalk structure protruding from one pole that has an adhesive holdfast material on its end, with which the stalked cell can adhere to surfaces. Swarmer cells differentiate into stalked cells after a short period of motility. Chromosome replication and cell division only occurs in

660-411: Is accomplished by the genetic regulatory circuit composed of five master regulators and an associated phospho-signaling network. The phosphosignaling network monitors the state of progression of the cell cycle and plays an essential role in accomplishing asymmetric cell division. The cell cycle control system manages the time and place of the initiation of chromosome replication and cytokinesis as well as

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720-453: Is dependent on this spatial organization. By the late 1990s, Shapiro and graduate student Michael Laub were able to study the genetic basis of cell cycle progression and consequently the identification of three regulatory proteins, DnaA, GcrA, and CtrA, which controlled complex temporal and spatial behaviors affecting large numbers of genes. With Dickon Alley and Janine Maddock, she showed that chemoreceptor proteins occupy specific areas within

780-421: Is readily apparent by the assembly of polar organelles and by the polarization of the division plane, which results in the generation of stalked progeny that are longer than swarmer progeny. The formation of new cell poles at division implies that cell polarity must be re-established in the stalked progeny and reversed in the swarmer progeny. The C. crescentus life cycle is governed by regulators such as TipN ,

840-510: Is still being investigated, it is likely that the stalks are involved in the uptake of nutrients in nutrient-limited conditions. Its use as a model originated with developmental biologist Lucy Shapiro . In the laboratory, researchers distinguish between C. crescentus strain CB15 (the strain originally isolated from a freshwater lake) and NA1000 (the primary experimental strain). In strain NA1000, which

900-511: Is synonymous with Caulobacter vibrioides . The Caulobacter CB15 genome has 4,016,942 base pairs in a single circular chromosome encoding 3,767 genes. The genome contains multiple clusters of genes encoding proteins essential for survival in a nutrient-poor habitat. Included are those involved in chemotaxis, outer membrane channel function, degradation of aromatic ring compounds, and the breakdown of plant-derived carbon sources, in addition to many extracytoplasmic function sigma factors, providing

960-472: Is that the chromosome is replicated once and only once per cell cycle. This is in contrast to the E. coli cell cycle where there can be overlapping rounds of chromosome replication simultaneously underway. The opposing roles of the Caulobacter DnaA and CtrA proteins are essential to the tight control of Caulobacter chromosome replication. The DnaA protein acts at the origin of replication to initiate

1020-404: Is unable to initiate DNA replication unless differentiated into a stalked cell. The differentiation process includes a morphological transition characterized by ejection of its flagellum and growth of a stalk at the same pole. Stalked cells can elongate and replicate their DNA while growing a flagellum at the opposite pole, giving rise to a pre-divisional cell. Although the precise function of stalks

1080-722: The Albert Einstein College of Medicine in 1966, with the thesis Replication of bacteriophage RNA. Shapiro has published reflections on her early days in Brooklyn and on her life in science in the Journal of Biological Chemistry and in the Annual Review of Genetics . Shapiro initially planned to do postdoctoral work elsewhere, but was offered a faculty position at Einstein by Bernard Horecker . Horecker proposed that she take three months to think about fundamental questions and

1140-643: The Albert Einstein College of Medicine from 1967–1986, as assistant professor, associate professor, and professor. In 1977, she became chair of the department of molecular biology and in 1981, director of Einstein's division of biological sciences. In 1983, she was named to the Lola and Saul Kramer Endowed Chair in Molecular Biology, Albert Einstein College of Medicine, NYC. From 1986–1989, Shapiro served as

1200-637: The Higgins Professor and Chair of Microbiology at the College of Physicians and Surgeons of Columbia University . In 1989, Shapiro became a professor and the founding chair of the department of developmental biology at Stanford University School of Medicine, Stanford, California. She was the Joseph D. Grant Professor in the school of medicine from 1989–1998, before becoming the Virginia and D.K. Ludwig Professor of Cancer Research in 1998. In 2001 Shapiro became

1260-451: The cell cycle control system. However, they can adapt, somewhat independently of the cell cycle control logic, to changing composition and levels of the available nutrient sources. The proteins of the Caulobacter cell cycle control system are widely co-conserved across the alphaproteobacteria, but the ultimate function of this regulatory system varies widely in different species. These evolutionary changes reflect enormous differences between

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1320-446: The cell cycle regulation is a cyclical genetic circuit—a cell cycle engine—that is centered around the successive interactions of five master regulatory proteins: DnaA, GcrA, CtrA, SciP, and CcrM whose roles were worked out by the laboratories of Lucy Shapiro and Harley McAdams . These five proteins directly control the timing of expression of over 200 genes. The five master regulatory proteins are synthesized and then eliminated from

1380-419: The cell cycle to ensure that changes occur at developmentally appropriate times. DNA is copied once per cycle by a particular group of molecules. Once a single DNA copy is placed in each half of the cell, other mechanisms constricts the cell's middle to separate it into two daughters. Shapiro was the first researcher to show that bacterial DNA replication occurs in a spatially organized way and that cell division

1440-453: The cell one after the other over the course of the cell cycle. Several additional cell signaling pathways are also essential to the proper functioning of this cell cycle engine. The principal role of these signaling pathways is to ensure reliable production and elimination of the CtrA protein from the cell at just the right times in the cell cycle. An essential feature of the Caulobacter cell cycle

1500-424: The cell. Shapiro and Christine Jacobs-Wagner as well as Janine Maddock showed that signaling phosphokinases also had specific positions at the cell poles. In 2004, using time-lapse microscopy and fluorescent tags, Shapiro demonstrated that chromosomal regions are duplicated in both an orderly and a location-specific manner, involving "a much higher degree of spatial organization than previously thought". By studying

1560-411: The chromosome, the actual reaction time for each reaction varies widely around the average rate. This leads to a significant and inevitable cell-to-cell variation time to complete replication of the chromosome. There is similar random variation in the rates of progression of all the other subsystem reaction cascades. The net effect is that the time to complete the cell cycle varies widely over the cells in

1620-434: The control subsystem interfaces with the environment by means of sensory modules largely located on the cell surface. The genetic network logic responds to signals received from the environment and from internal cell status sensors to adapt the cell to current conditions. A major function of the top level control is to ensure that the operations involved in the cell cycle occur in the proper temporal order. In Caulobacter , this

1680-426: The controlled system creates a closed loop control system. The rate of progression of the cell cycle is further adjusted by additional signals arising from cellular sensors that monitor environmental conditions (for example, nutrient levels and the oxygen level) or the internal cell status (for example, presence of DNA damage). The control circuitry that directs and paces Caulobacter cell cycle progression involves

1740-407: The development of polar organelles . Underlying all these operations are the mechanisms for production of protein and structural components and energy production. The “housekeeping” metabolic and catabolic subsystems provide the energy and the molecular raw materials for protein synthesis, cell wall construction and other operations of the cell. The housekeeping functions are coupled bidirectionally to

1800-403: The development of zoönotic diseases which travel from one species to another, such as influenza . To address either naturally occurring or intentionally developed biological threats, it is essential to understand the mechanisms involved internally in cells and in populations of cells in their environments. Shapiro emphasizes the importance of understanding the complexity of living systems, and

1860-440: The direction of her future research life. Shapiro identified positional information as a key research area, asking how spatial information is genetically encoded and translated, to create the three-dimensional organization of a cell and to form different daughter cells through cell division. With how a cell organizes its three-dimensional structure as her focus, Shapiro launched her own lab at Einstein in 1967. Shapiro remained at

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1920-465: The director of the Beckman Center for Molecular and Genetic Medicine at Stanford University School of Medicine. 'If you are confident in what you are talking about, and your science is excellent, there is no need to be intimidated by anyone,' says Shapiro. 'This is particularly important for women in science.' After six months as a postdoctoral student at Albert Einstein College of Medicine, Shapiro

1980-455: The entire cell operating as an integrated system. The control circuitry monitors the environment and the internal state of the cell, including the cell topology, as it orchestrates activation of cell cycle subsystems and Caulobacter crescentus asymmetric cell division. The proteins of the Caulobacter cell cycle control system and its internal organization are co-conserved across many alphaproteobacteria species, but there are great differences in

2040-536: The flagellar marker PodJ , and the stalk marker DivJ. Lucy Shapiro Shapiro founded a new field in developmental biology, using microorganisms to examine fundamental questions in developmental biology. Her work has furthered understanding of the basis of stem cell function and the generation of biological diversity. Her ideas have revolutionized understanding of bacterial genetic networks and helped researchers to develop novel drugs to fight antibiotic resistance and emerging infectious diseases. In 2013, Shapiro

2100-595: The genus are specialized to oligotrophic environments. Although Caulobacter is not commonly appreciated as a cause of human diseases, Caulobacter isolates have been implicated in a number of cases of recurrent peritonitis in peritoneal dialysis patients. One study has identified the species C. crescentus and C. mirare as the cause of a disease of the moth Galleria mellonella ; the absence of identified distinct virulence factors in C. mirare may suggest that other Caulobacter species have pathogenic potential. Caulobacter crescentus Caulobacter crescentus

2160-487: The identification of landmark proteins important for their proper localization. TipN has two transmembrane regions in the N-terminal region and a large C-terminal coiled-coil domain. TipN homologues are present in other alpha-proteobacteria. TipN localizes to the new pole in both daughter cells after division and relocalizes to the cell division site in the late predivisional cell. Therefore, both daughter cells have TipN at

2220-434: The individual species in fitness strategies and ecological niches. For example, Agrobacterium tumefaciens is a plant pathogen, Brucella abortus is an animal pathogen, and Sinorhizobium meliloti is a soil bacterium that invades, and becomes a symbiont in, plant root nodules that fix nitrogen yet most of the proteins of the Caulobacter cell cycle control are also found in these species. The specific coupling between

2280-494: The new pole after division. The landmark protein TipN is essential for the proper placement of the flagellum. Mutants lacking TipN make serious mistakes in development. Instead of making a single flagellum at the correct cell pole , the cell makes multiple flagella at various locations, even on the stalk. Cell development involves many such proteins working together. Fig#1 shows how TipN interact with two other polar proteins :

2340-405: The obligate dispersal stage must increase the reproductive fitness of the species as a whole. The Caulobacter cell cycle regulatory system controls many modular subsystems that organize the progression of cell growth and reproduction. A control system constructed using biochemical and genetic logic circuitry organizes the timing of initiation of each of these subsystems. The central feature of

2400-598: The organism with the ability to respond to a wide range of environmental fluctuations. In 2010, the Caulobacter NA1000 strain was sequenced and all differences with the CB15 "wild type" strain were identified. The Caulobacter stalked cell stage provides a fitness advantage by anchoring the cell to surfaces to form biofilms and or to exploit nutrient sources. Generally, the bacterial species that divides fastest will be most effective at exploiting resources and effectively occupying ecological niches. Yet, Caulobacter has

2460-445: The parent cell while the other does not. Since 1995, her work with Harley McAdams has applied insights and analysis techniques from the field of electrical circuitry to bacteria, to examine how biological systems work as a whole. Genome-based computational modelling, in particular, the examination of regulatory networks, is becoming increasingly important to systems biology . Examining the cell cycle control logic of Caulobacter as

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2520-415: The polarity axis, which is crucial for polar morphogenesis and division. Recruitment of TipN to the nascent poles at the end of the division cycle redefines the identity of the poles and resets the correct polarity in both future daughter cells (with a polarity reversal in the swarmer cell). The cell cycle–regulated synthesis and removal of these polarly localized structures have provided a rich playground for

2580-423: The predominant experimental Caulobacter strain throughout the world. Additional phenotypic differences between the two strains have subsequently accumulated due to selective pressures on the NA1000 strain in the laboratory environment. The genetic basis of the phenotypic differences between the two strains results from coding, regulatory, and insertion/deletion polymorphisms at five chromosomal loci. C. crescentus

2640-402: The protein components of the cell cycle control network and the downstream readout of the circuit differ from species to species. The pattern is that the internal functionality of the network circuitry is conserved, but the coupling at the “edges” of the regulatory apparatus to the proteins controlling specific cellular functions differs widely among the different species. Caulobacter crescentus

2700-430: The proteins of the cell cycle engine involve a cascade of many reactions. The longest subsystem cascade is DNA replication. In Caulobacter cells, replication of the chromosome involves about 2 million DNA synthesis reactions for each arm of the chromosome over 40 to 80 min depending on conditions. While the average time for each individual synthesis reaction can be estimated from the observed average total time to replicate

2760-513: The regulation of the cell cycle, asymmetric cell division, and cellular differentiation, Shapiro's work has led to a much deeper understanding of the genetic and molecular processes that cause identical bacterial cells to split into different cell types. These are basic processes that underlie all life, from single-cell bacteria to multi-cellular organisms. The process of the Caulobacter cell cycle also show similarities to stem cell division, in which two distinct cells arise, one of which differs from

2820-428: The regulatory apparatus' functionality and peripheral connectivity to other cellular subsystems from species to species. The Caulobacter cell cycle control system has been exquisitely optimized by evolutionary selection as a total system for robust operation in the face of internal stochastic noise and environmental uncertainty. The bacterial cell's control system has a hierarchical organization. The signaling and

2880-461: The replication of the chromosome. The CtrA protein, in contrast, acts to block initiation of replication, so it must be removed from the cell before chromosome replication can begin. Multiple additional regulatory pathways integral to cell cycle regulation and involving both phospho signaling pathways and regulated control of protein proteolysis act to assure that DnaA and CtrA are present in the cell just exactly when needed. Each process activated by

2940-579: The second Bush administration. She belongs to the Center for International Security and Cooperation at the Freeman Spogli Institute for International Studies at Stanford University. She is particularly concerned about the potential impact of emerging infectious diseases. There are a number of issues that make infectious diseases a particularly significant concern. One issue is the development of antibiotic-resistant microbes, which have been emerging as

3000-460: The simplest organism I could, and set out to learn how the multiple components of a living cell work together." She selected a single-celled organism, Caulobacter crescentus , and began attempting to identify the specific biological processes controlling the cell's cycle. What she and her students discovered overturned accepted beliefs about bacterial cell biology. In each cell cycle, Caulobacter divides asymmetrically into two daughters. One,

3060-517: The spatial properties of organic molecules in three dimensions. She received her A.B. in Fine Arts and Biology from Brooklyn College in 1962. In fall 1962 Shapiro was hired as a lab technician by J. Thomas August and Jerard Hurwitz in the department of microbiology at the New York University (NYU) school of medicine. Hurwitz was a co-discoverer of DNA-dependent RNA polymerase. Shapiro

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3120-401: The stalked cell stage. C. crescentus derives its name from its crescent shape, which is caused by the protein crescentin . It is an interesting organism to study because it inhabits nutrient-poor aquatic environments. Their ability to thrive in low levels of nutrients is facilitated by its dimorphic developmental cycle. The swarmer cell has a flagellum that protrudes from a single pole and

3180-413: The swarmer cell stage that results in slower population growth. The swarmer cell is thought to provide cell dispersal, so that the organism constantly seeks out new environments. This may be particularly useful in severely nutrient-limited environments when the scant resources available can be depleted very quickly. Many, perhaps most, of the swarmer daughter cells will not find a productive environment, but

3240-451: The swarmer cell, has a tail-like flagellum that helps it swim; the other daughter has a stalk which anchors it to a surface. Swarmer cells become stalked cells after a short period of motility. Chromosome replication and cell division only occur in stalked cells. Rather than containing an evenly dispersed mixture of proteins, the single celled Caulobacter resembles a highly organized factory, with specific "machinery" regulating each step in

3300-635: Was an elementary school teacher and her father, a Ukrainian immigrant. She attended New York City's High School of Music and Arts with a major in Fine Arts. Shapiro enrolled in Brooklyn College with a double major in Fine Arts and Biology and the intention of becoming a medical illustrator. As part of an experimental honors program she was able to design her own curriculum. With the encouragement of Theodore Shedlovsky , she talked her way into an honors organic chemistry class. There her spatial and scientific interests reinforced each other as she visualized

3360-403: Was asked to join the faculty and establish her own lab. Asked what she most wanted to work on, Shapiro decided that she was fascinated by how a one-dimensional genetic code, DNA , could be translated into three-dimensional organisms. Shapiro wanted to go beyond test-tube studies of extracted cell contents, and examine the three-dimensional structure and behavior of actual living cells. "I found

3420-554: Was derived from CB15 in the 1970s, the stalked and predivisional cells can be physically separated in the laboratory from new swarmer cells, while cell types from strain CB15 cannot be physically separated. The isolated swarmer cells can then be grown as a synchronized cell culture. Detailed study of the molecular development of these cells as they progress through the cell cycle has enabled researchers to understand Caulobacter cell cycle regulation in great detail. Due to this capacity to be physically synchronized, strain NA1000 has become

3480-513: Was given the task of looking for RNA-dependent RNA polymerase using F2 RNA phage from Norton Zinder . She was successful in detecting the activity of an enzyme copying RNA. In 1963 Shapiro became a graduate student at NYU with Tom August as her advisor. The department subsequently joined the newly created department of molecular biology at the Albert Einstein College of Medicine. Shapiro also attended summer courses at Cold Spring Harbor Laboratory (CSHL) on Long Island. Shapiro earned her Ph.D. at

3540-423: Was measured as the decline in the number of progeny produced over time. On the basis of experimental evolution studies in C. crescentus , Ackermann et al. suggested that aging is probably a fundamental property of all cellular organisms. A similar phenomenon has since been described in the bacterium Escherichia coli , which gives rise to morphologically similar daughter cells. In C. crescentus , cell polarity

3600-423: Was presented with the 2011 National Medal of Science . for "her pioneering discovery that the bacterial cell is controlled by an integrated genetic circuit functioning in time and space that serves as a systems engineering paradigm underlying cell differentiation and ultimately the generation of diversity in all organisms." Lucy Shapiro was born in Brooklyn, New York City, the eldest of three daughters. Her mother

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