• Keine Ergebnisse gefunden

Bibliography

139 Achaz, Guillaume, Eric Coissac, Pierre Netter, and Eduardo P. C. Rocha. 2003. “Associations between

Inverted Repeats and the Structural Evolution of Bacterial Genomes.” Genetics 164 (4): 1279–89.

Aldén, L., F. Demoling, and E. Bååth. 2001. “Rapid Method of Determining Factors Limiting Bacterial Growth in Soil.” Applied and Environmental Microbiology 67 (4): 1830–38.

Aldridge, Bree B., Marta Fernandez-Suarez, Danielle Heller, Vijay Ambravaneswaran, Daniel Irimia, Mehmet Toner, and Sarah M. Fortune. 2012. “Asymmetry and Aging of Mycobacterial Cells Lead to Variable Growth and Antibiotic Susceptibility.” Science 335 (6064): 100–104.

Amir, Ariel. 2014. “Cell Size Regulation in Bacteria.” Physical Review Letters 112 (20): 208102.

Anders, S., P. T. Pyl, and W. Huber. 2014. “HTSeq--a Python Framework to Work with High-Throughput Sequencing Data.” Bioinformatics , September. https://doi.org/10.1093/bioinformatics/btu638.

Aronesty, Erik. 2011. “Ea-Utils: Command-Line Tools for Processing Biological Sequencing Data.”

“Babraham Bioinformatics - FastQC A Quality Control Tool for High Throughput Sequence Data.” n.d.

Accessed July 27, 2015. http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/.

Baker, G. C., J. J. Smith, and D. A. Cowan. 2003. “Review and Re-Analysis of Domain-Specific 16S Primers.” Journal of Microbiological Methods 55 (3): 541–55.

Balleza, Enrique, Lucia N. López-Bojorquez, Agustino Martínez-Antonio, Osbaldo Resendis-Antonio, Irma Lozada-Chávez, Yalbi I. Balderas-Martínez, Sergio Encarnación, and Julio Collado-Vides.

2009. “Regulation by Transcription Factors in Bacteria: Beyond Description.” FEMS Microbiology Reviews 33 (1): 133–51.

Barka, Essaid Ait, Parul Vatsa, Lisa Sanchez, Nathalie Gaveau-Vaillant, Cedric Jacquard, Jan P. Meier-Kolthoff, Hans-Peter Klenk, Christophe Clément, Yder Ouhdouch, and Gilles P. van Wezel. 2016.

“Taxonomy, Physiology, and Natural Products of Actinobacteria.” Microbiology and Molecular Biology Reviews: MMBR 80 (1): 1–43.

Bejerano-Sagie, Michal, and Karina Bivar Xavier. 2007. “The Role of Small RNAs in Quorum Sensing.”

Current Opinion in Microbiology 10 (2): 189–98.

Biebricher, C. K., and M. Druminski. 1980. “Inhibition of RNA Polymerase Activity by the Escherichia Coli Protein Biosynthesis Elongation Factor Ts.” Proceedings of the National Academy of Sciences of the United States of America 77 (2): 866–69.

Bonner, E. R., J. N. D’Elia, B. K. Billips, and R. L. Switzer. 2001. “Molecular Recognition of Pyr mRNA by the Bacillus Subtilis Attenuation Regulatory Protein PyrR.” Nucleic Acids Research 29 (23):

4851–65.

Borkowski, Olivier, Anne Goelzer, Marc Schaffer, Magali Calabre, Ulrike Mäder, Stéphane Aymerich, Matthieu Jules, and Vincent Fromion. 2016. “Translation Elicits a Growth Rate-Dependent, Genome-Wide, Differential Protein Production in Bacillus Subtilis.” Molecular Systems Biology 12 (5): 870.

Bouhss, A., D. Mengin-Lecreulx, D. Blanot, J. van Heijenoort, and C. Parquet. 1997. “Invariant Amino Acids in the Mur Peptide Synthetases of Bacterial Peptidoglycan Synthesis and Their Modification by Site-Directed Mutagenesis in the UDP-MurNAc:L-Alanine Ligase from Escherichia Coli.”

Biochemistry 36 (39): 11556–63.

Bramkamp, Marc, Louise Weston, Richard A. Daniel, and Jeff Errington. 2006. “Regulated

Intramembrane Proteolysis of FtsL Protein and the Control of Cell Division in Bacillus Subtilis.”

Molecular Microbiology 62 (2): 580–91.

Bremer, Hans, and Patrick P. Dennis. 2008. “Modulation of Chemical Composition and Other Parameters of the Cell at Different Exponential Growth Rates.” EcoSal Plus 3 (1).

https://doi.org/10.1128/ecosal.5.2.3.

Broman, K., N. Lauwers, V. Stalon, and J. M. Wiame. 1978. “Oxygen and Nitrate in Utilization by Bacillus Licheniformis of the Arginase and Arginine Deiminase Routes of Arginine Catabolism and Other Factors Affecting Their Syntheses.” Journal of Bacteriology 135 (3): 920–27.

Brown, Stephanie, John P. Santa Maria Jr, and Suzanne Walker. 2013. “Wall Teichoic Acids of Gram-Positive Bacteria.” Annual Review of Microbiology 67: 313–36.

Bügl, H., E. B. Fauman, B. L. Staker, F. Zheng, S. R. Kushner, M. A. Saper, J. C. Bardwell, and U. Jakob.

2000. “RNA Methylation under Heat Shock Control.” Molecular Cell 6 (2): 349–60.

Bibliography

140 Calderón, Iván L., Eduardo H. Morales, Bernardo Collao, Paulina F. Calderón, Catalina A. Chahuán,

Lillian G. Acuña, Fernando Gil, and Claudia P. Saavedra. 2014. “Role of Salmonella Typhimurium Small RNAs RyhB-1 and RyhB-2 in the Oxidative Stress Response.” Research in Microbiology 165 (1): 30–40.

Camacho, Christiam, George Coulouris, Vahram Avagyan, Ning Ma, Jason Papadopoulos, Kevin Bealer, and Thomas L. Madden. 2009. “BLAST+: Architecture and Applications.” BMC Bioinformatics 10 (December): 421.

Campos, Manuel, Ivan V. Surovtsev, Setsu Kato, Ahmad Paintdakhi, Bruno Beltran, Sarah E. Ebmeier, and Christine Jacobs-Wagner. 2014. “A Constant Size Extension Drives Bacterial Cell Size Homeostasis.” Cell 159 (6): 1433–46.

Cao, Min, Bryan A. Bernat, Zhepeng Wang, Richard N. Armstrong, and John D. Helmann. 2001. “FosB, a Cysteine-Dependent Fosfomycin Resistance Protein under the Control of ςW, an Extracytoplasmic-Function ς Factor in Bacillus Subtilis.” Journal of Bacteriology 183 (7): 2380–83.

Chang, D. E., S. Shin, J. S. Rhee, and J. G. Pan. 1999. “Acetate Metabolism in a Pta Mutant of Escherichia Coli W3110: Importance of Maintaining Acetyl Coenzyme A Flux for Growth and Survival.” Journal of Bacteriology 181 (21): 6656–63.

Chatterji, D., and A. K. Ojha. 2001. “Revisiting the Stringent Response, ppGpp and Starvation Signaling.”

Current Opinion in Microbiology 4 (2): 160–65.

Chen, I-Min A., Ken Chu, Krishna Palaniappan, Manoj Pillay, Anna Ratner, Jinghua Huang, Marcel Huntemann, et al. 2019. “IMG/M v.5.0: An Integrated Data Management and Comparative Analysis System for Microbial Genomes and Microbiomes.” Nucleic Acids Research 47 (D1): D666–77.

Cho, Byung-Kwan, Stephen Federowicz, Young-Seoub Park, Karsten Zengler, and Bernhard Ø. Palsson.

2011. “Deciphering the Transcriptional Regulatory Logic of Amino Acid Metabolism.” Nature Chemical Biology 8 (1): 65–71.

Chong, Jasmine, David S. Wishart, and Jianguo Xia. 2019. “Using MetaboAnalyst 4.0 for Comprehensive and Integrative Metabolomics Data Analysis.” Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [et Al.] 68 (1): 375.

Cingolani, Pablo, Adrian Platts, Le Lily Wang, Melissa Coon, Tung Nguyen, Luan Wang, Susan J. Land, Xiangyi Lu, and Douglas M. Ruden. 2012. “A Program for Annotating and Predicting the Effects of Single Nucleotide Polymorphisms, SnpEff: SNPs in the Genome of Drosophila Melanogaster Strain w1118; Iso-2; Iso-3.” Fly 6 (2): 80–92.

Cooper, S., and C. E. Helmstetter. 1968. “Chromosome Replication and the Division Cycle of Escherichia Coli B/r.” Journal of Molecular Biology 31 (3): 519–40.

Couturier, Etienne, and Eduardo P. C. Rocha. 2006. “Replication-Associated Gene Dosage Effects Shape the Genomes of Fast-Growing Bacteria but Only for Transcription and Translation Genes.”

Molecular Microbiology 59 (5): 1506–18.

Cox, Murray P., Daniel A. Peterson, and Patrick J. Biggs. 2010. “SolexaQA: At-a-Glance Quality

Assessment of Illumina Second-Generation Sequencing Data.” BMC Bioinformatics 11 (September):

485.

Crawford, Evan C., Ameet Singh, Devon Metcalf, Thomas W. G. Gibson, and Scott J. Weese. 2014.

“Identification of Appropriate Reference Genes for qPCR Studies in Staphylococcus

Pseudintermedius and Preliminary Assessment of icaA Gene Expression in Biofilm-Embedded Bacteria.” BMC Research Notes 7 (July): 451.

Cunin, R., N. Glansdorff, A. Piérard, and V. Stalon. 1986. “Biosynthesis and Metabolism of Arginine in Bacteria.” Microbiological Reviews 50 (3): 314–52.

Czaplewski, L. G., A. K. North, M. C. Smith, S. Baumberg, and P. G. Stockley. 1992. “Purification and Initial Characterization of AhrC: The Regulator of Arginine Metabolism Genes in Bacillus Subtilis.”

Molecular Microbiology 6 (2): 267–75.

Dai, Xiongfeng, Zichu Shen, Yiheng Wang, and Manlu Zhu. 2018. “Sinorhizobium Meliloti, a Slow-Growing Bacterium, Exhibits Growth Rate Dependence of Cell Size under Nutrient Limitation.”

mSphere 3 (6). https://doi.org/10.1128/mSphere.00567-18.

Bibliography

141 Dandekar, T., B. Snel, M. Huynen, and P. Bork. 1998. “Conservation of Gene Order: A Fingerprint of

Proteins That Physically Interact.” Trends in Biochemical Sciences 23 (9): 324–28.

Darling, Aaron E., István Miklós, and Mark A. Ragan. 2008. “Dynamics of Genome Rearrangement in Bacterial Populations.” PLoS Genetics 4 (7): e1000128.

Daubin, Vincent, Emmanuelle Lerat, and Guy Perrière. 2003. “The Source of Laterally Transferred Genes in Bacterial Genomes.” Genome Biology 4 (9): R57.

Dehal, Paramvir S., Marcin P. Joachimiak, Morgan N. Price, John T. Bates, Jason K. Baumohl, Dylan Chivian, Greg D. Friedland, et al. 2010. “MicrobesOnline: An Integrated Portal for Comparative and Functional Genomics.” Nucleic Acids Research 38 (Database issue): D396–400.

Derbyshire, Keith M., and Todd A. Gray. 2014. “Distributive Conjugal Transfer: New Insights into Horizontal Gene Transfer and Genetic Exchange in Mycobacteria.” Microbiology Spectrum 2 (1).

https://doi.org/10.1128/microbiolspec.MGM2-0022-2013.

Dillingham, Mark S., and Stephen C. Kowalczykowski. 2008. “RecBCD Enzyme and the Repair of Double-Stranded DNA Breaks.” Microbiology and Molecular Biology Reviews: MMBR 72 (4): 642–

71, Table of Contents.

Donachie, W. D. 1968. “Relationship between Cell Size and Time of Initiation of DNA Replication.”

Nature 219 (5158): 1077–79.

Dong, Hengjiang, Lars Nilsson, and Charles G. Kurland. 1996. “Co-Variation of tRNA Abundance and Codon Usage inEscherichia Coliat Different Growth Rates.” Journal of Molecular Biology 260 (5):

649–63.

Dorman, Charles J. 2006. “DNA Supercoiling and Bacterial Gene Expression.” Science Progress 89 (Pt 3-4): 151–66.

Eddy, S. R. 2001. “Non-Coding RNA Genes and the Modern RNA World.” Nature Reviews. Genetics 2 (12): 919–29.

Eiamphungporn, Warawan, and John D. Helmann. 2008. “The Bacillus Subtilis sigma(M) Regulon and Its Contribution to Cell Envelope Stress Responses.” Molecular Microbiology 67 (4): 830–48.

El-Gebali, Sara, Jaina Mistry, Alex Bateman, Sean R. Eddy, Aurélien Luciani, Simon C. Potter, Matloob Qureshi, et al. 2019. “The Pfam Protein Families Database in 2019.” Nucleic Acids Research 47 (D1): D427–32.

Eren, A. Murat, Loïs Maignien, Woo Jun Sul, Leslie G. Murphy, Sharon L. Grim, Hilary G. Morrison, and Mitchell L. Sogin. 2013. “Oligotyping: Differentiating between Closely Related Microbial Taxa Using 16S rRNA Gene Data.” Methods in Ecology and Evolution / British Ecological Society 4 (12).

https://doi.org/10.1111/2041-210X.12114.

Fadda, Daniela, Carla Pischedda, Fabrizio Caldara, Michael B. Whalen, Daniela Anderluzzi, Enrico Domenici, and Orietta Massidda. 2003. “Characterization of divIVA and Other Genes Located in the Chromosomal Region Downstream of the Dcw Cluster in Streptococcus Pneumoniae.” Journal of Bacteriology 185 (20): 6209–14.

Fang, Gang, Eduardo P. C. Rocha, and Antoine Danchin. 2008. “Persistence Drives Gene Clustering in Bacterial Genomes.” BMC Genomics 9 (January): 4.

Fani, Renato, Matteo Brilli, and Pietro Liò. 2005. “The Origin and Evolution of Operons: The Piecewise Building of the Proteobacterial Histidine Operon.” Journal of Molecular Evolution 60 (3): 378–90.

Fiil, N., and J. D. Friesen. 1968. “Isolation of ‘Relaxed’ Mutants of Escherichia Coli.” Journal of Bacteriology 95 (2): 729–31.

Fisher, R. A. 1929. The Genetical Theory of Natural Selection. Edinburgh: Oliver & Boyd.

Fondi, Marco, Giovanni Emiliani, and Renato Fani. 2009. “Origin and Evolution of Operons and Metabolic Pathways.” Research in Microbiology 160 (7): 502–12.

Fourment, Mathieu, and Mark J. Gibbs. 2006. “PATRISTIC: A Program for Calculating Patristic Distances and Graphically Comparing the Components of Genetic Change.” BMC Evolutionary Biology 6 (January): 1.

Francis, F., S. Ramirez-Arcos, H. Salimnia, C. Victor, and J. R. Dillon. 2000. “Organization and

Transcription of the Division Cell Wall (dcw) Cluster in Neisseria Gonorrhoeae.” Gene 251 (2): 141–

Bibliography

142 51.

Fuente, A. de la, P. Palacios, and M. Vicente. 2001. “Transcription of the Escherichia Coli Dcw Cluster:

Evidence for Distal Upstream Transcripts Being Involved in the Expression of the Downstream ftsZ Gene.” Biochimie 83 (1): 109–15.

Fukuda, Yoko, Yoichi Nakayama, and Masaru Tomita. 2003. “On Dynamics of Overlapping Genes in Bacterial Genomes.” Gene 323 (December): 181–87.

Gaal, T., M. S. Bartlett, W. Ross, C. L. Turnbough Jr, and R. L. Gourse. 1997. “Transcription Regulation by Initiating NTP Concentration: rRNA Synthesis in Bacteria.” Science 278 (5346): 2092–97.

Gagyi, Cristina, Nadia Bucurenci, Ovidiu Sîrbu, Gilles Labesse, Mihaela Ionescu, Augustin Ofiteru, Liliane Assairi, et al. 2003. “UMP Kinase from the Gram-Positive Bacterium Bacillus Subtilis Is Strongly Dependent on GTP for Optimal Activity.” European Journal of Biochemistry / FEBS 270 (15): 3196–3204.

Gagyi, Cristina, Mihaela Ionescu, Pierre Gounon, Hiroshi Sakamoto, Jean-Claude Rousselle, and

Christine Laurent-Winter. 2004. “Identification and Immunochemical Location of UMP Kinase from Bacillus Subtilis.” Current Microbiology 48 (1): 62–67.

Ganong, B. R., J. M. Leonard, and C. R. Raetz. 1980. “Phosphatidic Acid Accumulation in the

Membranes of Escherichia Coli Mutants Defective in CDP-Diglyceride Synthetase.” The Journal of Biological Chemistry 255 (4): 1623–29.

Gardan, R., G. Rapoport, and M. Débarbouillé. 1995. “Expression of the rocDEF Operon Involved in Arginine Catabolism in Bacillus Subtilis.” Journal of Molecular Biology 249 (5): 843–56.

Gärtner, D., J. Degenkolb, J. A. Ripperger, R. Allmansberger, and W. Hillen. 1992. “Regulation of the Bacillus Subtilis W23 Xylose Utilization Operon: Interaction of the Xyl Repressor with the Xyl Operator and the Inducer Xylose.” Molecular & General Genetics: MGG 232 (3): 415–22.

Geiman, Theresa M., and Keith D. Robertson. 2002. “Chromatin Remodeling, Histone Modifications, and DNA Methylation-How Does It All Fit Together?” Journal of Cellular Biochemistry 87 (2): 117–25.

Gerasimova, T. I., and V. G. Corces. 2001. “Chromatin Insulators and Boundaries: Effects on Transcription and Nuclear Organization.” Annual Review of Genetics 35: 193–208.

Gerlt, John A., Jason T. Bouvier, Daniel B. Davidson, Heidi J. Imker, Boris Sadkhin, David R. Slater, and Katie L. Whalen. 2015. “Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A Web Tool for Generating Protein Sequence Similarity Networks.” Biochimica et Biophysica Acta 1854 (8): 1019–37.

Ginez, Luis David, Aurora Osorio, and Sebastian Poggio. 2014. “Localization of the Outer Membrane Protein OmpA2 in Caulobacter Crescentus Depends on the Position of the Gene in the

Chromosome.” Journal of Bacteriology 196 (15): 2889–2900.

Gomes, Ana Érika Inácio, Leonardo Prado Stuchi, Nathália Maria Gonçalves Siqueira, João Batista Henrique, Renato Vicentini, Marcelo Lima Ribeiro, Michelle Darrieux, and Lúcio Fábio Caldas Ferraz. 2018. “Selection and Validation of Reference Genes for Gene Expression Studies in Klebsiella Pneumoniae Using Reverse Transcription Quantitative Real-Time PCR.” Scientific Reports 8 (1): 9001.

Gómez, Manuel J., Ildefonso Cases, and Alfonso Valencia. 2004. “Gene Order in Prokaryotes:

Conservation and Implications.” In Molecules in Time and Space: Bacterial Shape, Division and Phylogeny, edited by Miguel Vicente, Javier Tamames, Alfonso Valencia, and Jesús Mingorance, 209–37. Boston, MA: Springer US.

Gorle, Anil K., Amy L. Bottomley, Elizabeth J. Harry, J. Grant Collins, F. Richard Keene, and Clifford E.

Woodward. 2017. “DNA Condensation in Live E. Coli Provides Evidence for Transertion.”

Molecular bioSystems 13 (4): 677–80.

Grigoriev, Igor V., Henrik Nordberg, Igor Shabalov, Andrea Aerts, Mike Cantor, David Goodstein, Alan Kuo, et al. 2012. “The Genome Portal of the Department of Energy Joint Genome Institute.” Nucleic Acids Research 40 (Database issue): D26–32.

Gromadski, Kirill B., Hans-Joachim Wieden, and Marina V. Rodnina. 2002. “Kinetic Mechanism of Elongation Factor Ts-Catalyzed Nucleotide Exchange in Elongation Factor Tu.” Biochemistry 41 (1):

Bibliography

143 162–69.

Hahne, Hannes, Susanne Wolff, Michael Hecker, and Dörte Becher. 2008. “From Complementarity to Comprehensiveness--Targeting the Membrane Proteome of Growing Bacillus Subtilis by Divergent Approaches.” Proteomics 8 (19): 4123–36.

Hamoen, Leendert W., Jean-Christophe Meile, Wouter de Jong, Philippe Noirot, and Jeff Errington. 2006.

“SepF, a Novel FtsZ-Interacting Protein Required for a Late Step in Cell Division.” Molecular Microbiology 59 (3): 989–99.

Helmann, John D. 2006. “Deciphering a Complex Genetic Regulatory Network: The Bacillus Subtilis sigmaW Protein and Intrinsic Resistance to Antimicrobial Compounds.” Science Progress 89 (Pt 3-4): 243–66.

Hernández-Tamayo, Rogelio, Luis M. Oviedo-Bocanegra, Georg Fritz, and Peter L. Graumann. 2019.

“Symmetric Activity of DNA Polymerases at and Recruitment of Exonuclease ExoR and of PolA to the Bacillus Subtilis Replication Forks.” Nucleic Acids Research, June.

https://doi.org/10.1093/nar/gkz554.

Hershberg, Ruth, and Dmitri A. Petrov. 2010. “Evidence That Mutation Is Universally Biased towards AT in Bacteria.” PLoS Genetics 6 (9): e1001115.

Hess, Becky M., Junfeng Xue, Lye Meng Markillie, Ronald C. Taylor, H. Steven Wiley, Birgitte K.

Ahring, and Bryan Linggi. 2013. “Coregulation of Terpenoid Pathway Genes and Prediction of Isoprene Production in Bacillus Subtilis Using Transcriptomics.” PloS One 8 (6): e66104.

Hill, Norbert S., Paul J. Buske, Yue Shi, and Petra Anne Levin. 2013. “A Moonlighting Enzyme Links Escherichia Coli Cell Size with Central Metabolism.” PLoS Genetics 9 (7): e1003663.

Hill, Norbert S., Ryosuke Kadoya, Dhruba K. Chattoraj, and Petra Anne Levin. 2012. “Cell Size and the Initiation of DNA Replication in Bacteria.” PLoS Genetics 8 (3): e1002549.

Hobl, Birgit, and Matthias Mack. 2007. “The Regulator Protein PyrR of Bacillus Subtilis Specifically Interacts in Vivo with Three Untranslated Regions within Pyr mRNA of Pyrimidine Biosynthesis.”

Microbiology 153 (Pt 3): 693–700.

Hoffart, Eugenia, Sebastian Grenz, Julian Lange, Robert Nitschel, Felix Müller, Andreas Schwentner, André Feith, Mira Lenfers-Lücker, Ralf Takors, and Bastian Blombach. 2017. “High Substrate Uptake Rates Empower Vibrio Natriegens as Production Host for Industrial Biotechnology.” Applied and Environmental Microbiology 83 (22). https://doi.org/10.1128/AEM.01614-17.

House, Christopher H., Matteo Pellegrini, and Sorel T. Fitz-Gibbon. 2014. “Genome-Wide Gene Order Distances Support Clustering the Gram-Positive Bacteria.” Frontiers in Microbiology 5: 785.

Huang, Da Wei, Brad T. Sherman, and Richard A. Lempicki. 2009. “Systematic and Integrative Analysis of Large Gene Lists Using DAVID Bioinformatics Resources.” Nature Protocols 4 (1): 44–57.

Huang, Xiaoluo, Daniela Pinto, Georg Fritz, and Thorsten Mascher. 2015. “Environmental Sensing in Actinobacteria: A Comprehensive Survey on the Signaling Capacity of This Phylum.” Journal of Bacteriology 197 (15): 2517–35.

Huberts, Daphne H. E. W., and Ida J. van der Klei. 2010. “Moonlighting Proteins: An Intriguing Mode of Multitasking.” Biochimica et Biophysica Acta 1803 (4): 520–25.

Huynen, M., B. Snel, W. Lathe 3rd, and P. Bork. 2000. “Predicting Protein Function by Genomic Context:

Quantitative Evaluation and Qualitative Inferences.” Genome Research 10 (8): 1204–10.

Itaya, M., A. Omori, S. Kanaya, R. J. Crouch, T. Tanaka, and K. Kondo. 1999. “Isolation of RNase H Genes That Are Essential for Growth of Bacillus Subtilis 168.” Journal of Bacteriology 181 (7):

2118–23.

Itoh, T., K. Takemoto, H. Mori, and T. Gojobori. 1999. “Evolutionary Instability of Operon Structures Disclosed by Sequence Comparisons of Complete Microbial Genomes.” Molecular Biology and Evolution 16 (3): 332–46.

Jacob, F., and J. Monod. 1961. “Genetic Regulatory Mechanisms in the Synthesis of Proteins.” Journal of Molecular Biology 3 (June): 318–56.

Jain, Vikas, Manish Kumar, and Dipankar Chatterji. 2006. “ppGpp: Stringent Response and Survival.”

Journal of Microbiology 44 (1): 1–10.

Bibliography

144 Janga, Sarath Chandra, Warren F. Lamboy, Araceli M. Huerta, and Gabriel Moreno-Hagelsieb. 2006.

“The Distinctive Signatures of Promoter Regions and Operon Junctions across Prokaryotes.” Nucleic Acids Research 34 (14): 3980–87.

Janosi, L., I. Shimizu, and A. Kaji. 1994. “Ribosome Recycling Factor (ribosome Releasing Factor) Is Essential for Bacterial Growth.” Proceedings of the National Academy of Sciences of the United States of America 91 (10): 4249–53.

Jogler, Christian, Jost Waldmann, Xiaoluo Huang, Mareike Jogler, Frank Oliver Glöckner, Thorsten Mascher, and Roberto Kolter. 2012. “Identification of Proteins Likely to Be Involved in Morphogenesis, Cell Division, and Signal Transduction in Planctomycetes by Comparative Genomics.” Journal of Bacteriology 194 (23): 6419–30.

Jordan, Sina, Anja Junker, John D. Helmann, and Thorsten Mascher. 2006. “Regulation of LiaRS-Dependent Gene Expression in Bacillus Subtilis: Identification of Inhibitor Proteins, Regulator Binding Sites, and Target Genes of a Conserved Cell Envelope Stress-Sensing Two-Component System.” Journal of Bacteriology 188 (14): 5153–66.

Joseph, Pascale, Gwennaele Fichant, Yves Quentin, and François Denizot. 2002. “Regulatory Relationship of Two-Component and ABC Transport Systems and Clustering of Their Genes in the

Bacillus/Clostridium Group, Suggest a Functional Link between Them.” Journal of Molecular Microbiology and Biotechnology 4 (5): 503–13.

Kabeya, Yukihiro, Hiromitsu Nakanishi, Kenji Suzuki, Takanari Ichikawa, Youichi Kondou, Minami Matsui, and Shin-Ya Miyagishima. 2010. “The YlmG Protein Has a Conserved Function Related to the Distribution of Nucleoids in Chloroplasts and Cyanobacteria.” BMC Plant Biology 10 (April): 57.

Kaminishi, Tatsuya, Daniel N. Wilson, Chie Takemoto, Joerg M. Harms, Masahito Kawazoe, Frank Schluenzen, Kyoko Hanawa-Suetsugu, Mikako Shirouzu, Paola Fucini, and Shigeyuki Yokoyama.

2007. “A Snapshot of the 30S Ribosomal Subunit Capturing mRNA via the Shine-Dalgarno Interaction.” Structure 15 (3): 289–97.

Kapitonov, Vladimir V., and Jerzy Jurka. 2008. “A Universal Classification of Eukaryotic Transposable Elements Implemented in Repbase.” Nature Reviews. Genetics.

Keseler, Ingrid M., Amanda Mackie, Alberto Santos-Zavaleta, Richard Billington, César Bonavides-Martínez, Ron Caspi, Carol Fulcher, et al. 2017. “The EcoCyc Database: Reflecting New Knowledge about Escherichia Coli K-12.” Nucleic Acids Research 45 (D1): D543–50.

Kim, L., A. Mogk, and W. Schumann. 1996. “A Xylose-Inducible Bacillus Subtilis Integration Vector and Its Application.” Gene 181 (1-2): 71–76.

Kingston, A. W., C. Subramanian, and C. O. Rock. 2011. “A σW‐dependent Stress Response in Bacillus Subtilis That Reduces Membrane Fluidity.” Molecular.

https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-2958.2011.07679.x.

Kleerebezemab, M., P. Hols, and J. Hugenholtz. 2000. “Lactic Acid Bacteria as a Cell Factory: Rerouting of Carbon Metabolism in Lactococcus Lactis by Metabolic Engineering.” Enzyme and Microbial Technology 26 (9-10): 840–48.

Koch, A. L. 1985. “How Bacteria Grow and Divide in Spite of Internal Hydrostatic Pressure.” Canadian Journal of Microbiology 31 (12): 1071–84.

Koshland, Daniel E., Jr. 2002. “Special Essay. The Seven Pillars of Life.” Science 295 (5563): 2215–16.

Kriventseva, Evgenia V., Dmitry Kuznetsov, Fredrik Tegenfeldt, Mosè Manni, Renata Dias, Felipe A.

Simão, and Evgeny M. Zdobnov. 2019. “OrthoDB v10: Sampling the Diversity of Animal, Plant, Fungal, Protist, Bacterial and Viral Genomes for Evolutionary and Functional Annotations of Orthologs.” Nucleic Acids Research 47 (D1): D807–11.

Kriventseva, Evgenia V., Fredrik Tegenfeldt, Tom J. Petty, Robert M. Waterhouse, Felipe A. Simão, Igor A. Pozdnyakov, Panagiotis Ioannidis, and Evgeny M. Zdobnov. 2015. “OrthoDB v8: Update of the Hierarchical Catalog of Orthologs and the Underlying Free Software.” Nucleic Acids Research 43 (Database issue): D250–56.

Kuroda, A., K. Nomura, R. Ohtomo, J. Kato, T. Ikeda, N. Takiguchi, H. Ohtake, and A. Kornberg. 2001.

“Role of Inorganic Polyphosphate in Promoting Ribosomal Protein Degradation by the Lon Protease

Bibliography

145 in E. Coli.” Science 293 (5530): 705–8.

Lachner, Monika, and Thomas Jenuwein. 2002. “The Many Faces of Histone Lysine Methylation.”

Current Opinion in Cell Biology 14 (3): 286–98.

Laing, Emma, Vassilis Mersinias, Colin P. Smith, and Simon J. Hubbard. 2006. “Analysis of Gene Expression in Operons of Streptomyces Coelicolor.” Genome Biology 7 (6): R46.

Langmead, Ben, and Steven L. Salzberg. 2012. “Fast Gapped-Read Alignment with Bowtie 2.” Nature Methods 9 (4): 357–59.

Lathe, W. C., 3rd, B. Snel, and P. Bork. 2000. “Gene Context Conservation of a Higher Order than Operons.” Trends in Biochemical Sciences 25 (10): 474–79.

Lawrence, J. 1999. “Selfish Operons: The Evolutionary Impact of Gene Clustering in Prokaryotes and Eukaryotes.” Current Opinion in Genetics & Development 9 (6): 642–48.

Lawrence, J. G., and J. R. Roth. 1996. “Selfish Operons: Horizontal Transfer May Drive the Evolution of Gene Clusters.” Genetics 143 (4): 1843–60.

Lechner, Marcus, Sven Findeiss, Lydia Steiner, Manja Marz, Peter F. Stadler, and Sonja J. Prohaska.

2011. “Proteinortho: Detection of (co-)orthologs in Large-Scale Analysis.” BMC Bioinformatics 12 (April): 124.

Lewin, Gina R., Camila Carlos, Marc G. Chevrette, Heidi A. Horn, Bradon R. McDonald, Robert J.

Stankey, Brian G. Fox, and Cameron R. Currie. 2016. “Evolution and Ecology of Actinobacteria and Their Bioenergy Applications.” Annual Review of Microbiology 70 (September): 235–54.

Lewis, P. J., S. D. Thaker, and J. Errington. 2000. “Compartmentalization of Transcription and Translation in Bacillus Subtilis.” The EMBO Journal 19 (4): 710–18.

Libby, Elizabeth A., Manuela Roggiani, and Mark Goulian. 2012. “Membrane Protein Expression Triggers Chromosomal Locus Repositioning in Bacteria.” Proceedings of the National Academy of Sciences of the United States of America 109 (19): 7445–50.

Li, Heng, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, and 1000 Genome Project Data Processing Subgroup. 2009. “The Sequence Alignment/Map Format and SAMtools.” Bioinformatics 25 (16): 2078–79.

Lin, Jie, and Ariel Amir. 2017. “The Effects of Stochasticity at the Single-Cell Level and Cell Size Control on the Population Growth.” Cell Systems 5 (4): 358–67.e4.

Lorenzo, V. de, and J. Pérez-Martín. 1996. “Regulatory Noise in Prokaryotic Promoters: How Bacteria Learn to Respond to Novel Environmental Signals.” Molecular Microbiology 19 (6): 1177–84.

Lu, Chung-Dar. 2006. “Pathways and Regulation of Bacterial Arginine Metabolism and Perspectives for Obtaining Arginine Overproducing Strains.” Applied Microbiology and Biotechnology 70 (3): 261–

72.

Lu, M., J. L. Campbell, E. Boye, and N. Kleckner. 1994. “SeqA: A Negative Modulator of Replication Initiation in E. Coli.” Cell 77 (3): 413–26.

Luo, Hao, Yan Lin, Feng Gao, Chun-Ting Zhang, and Ren Zhang. 2014. “DEG 10, an Update of the Database of Essential Genes That Includes Both Protein-Coding Genes and Noncoding Genomic Elements.” Nucleic Acids Research 42 (Database issue): D574–80.

Maeda, H., N. Fujita, and A. Ishihama. 2000. “Competition among Seven Escherichia Coli Sigma Subunits: Relative Binding Affinities to the Core RNA Polymerase.” Nucleic Acids Research 28 (18): 3497–3503.

Mao, Fenglou, Phuongan Dam, Jacky Chou, Victor Olman, and Ying Xu. 2009. “DOOR: A Database for Prokaryotic Operons.” Nucleic Acids Research 37 (Database issue): D459–63.

Matsumoto, Kouji, Hiroshi Hara, Itzhak Fishov, Eugenia Mileykovskaya, and Vic Norris. 2015. “The Membrane: Transertion as an Organizing Principle in Membrane Heterogeneity.” Frontiers in Microbiology 6 (June): 572.

Ma, Zheng, Libin Tao, Andreas Bechthold, Xuping Shentu, Yalin Bian, and Xiaoping Yu. 2014.

“Overexpression of Ribosome Recycling Factor Is Responsible for Improvement of Nucleotide Antibiotic-Toyocamycin in Streptomyces Diastatochromogenes 1628.” Applied Microbiology and Biotechnology 98 (11): 5051–58.