Molecular Biology

Genomics, DNA transfer, and Miscellaneous

RNA and transcription

DNA metabolism and plasmids

Protein metabolism, folding, and transport


Genomics, DNA transfer, and Miscellaneous

Aoyama K, Miyake M, Yamada J, Miyake J, Uemura I, Hoshino T, Asada Y (1996). Application of vector pKE4-9 carrying a strong promoter to the expression of foreign proteins in Synechococcus PCC7942. J Mar Biotechnol 4:64-67

Field D, Wills C (1998). Abundant microsatellite polymorphism in Saccharomyces cerevisiae, and the different distributions of microsatellites in eight prokaryotes and S. cerevisiae, result from strong mutation pressures and a variety of selective forces. Proc Natl Acad Sci USA 95:1647-1652

Geisler M, Jakobs B, Richter J, Schumann J (1996). Cotranscription of a GTPase gene from the cyanobacterium Synechocystis PCC 6803 and a P-type Ca-2+-ATPase gene. Biochim Biophys Acta 1309:189-193

Hirosawa M, Isono K, Hayes W, Borodovsky M (1997). Gene identification and classification in the Synechocystis genomic sequence by recursive gene mark analysis. DNA Sequence 8:17-29

Huynen MA, van Nimwegen E (1998). The frequency distribution of gene family sizes in complete genomes. Molec Biol Evol 15:583-589

Kaneko T, Kotani H, Tabata S (1997). Genome analysis of the cyanobacterium, Synechocystis sp. PCC6803. Tanpakushitsu Kakusan Koso - Protein, Nucleic Acid, Enzyme 42(17, Suppl):2946-2952 (Japanese)

Kaneko T, Tabata S (1997). Complete genome structure of the unicellular cyanobacterium Synechocystis sp. PCC6803. Plant Cell Physiol 38:1171-1176

Kuritz T, Wolk CP (1997) Localizing genes by the introduction of rare restriction sites. In: de Bruijn FJ, Lupski JR, Weinstock GM (eds) Bacterial Genomes: Physical Structure and Analysis. Chapman & Hall, New York

Miyake M, Yamada J, Aoyama K, Uemura I, Hoshino T, Miyake J, Asada Y (1996). Strong expression of foreign protein in Synechococcus PCC7942. J Mar Biotechnol 4:61-63

Nakamura Y, Kaneko T, Hirosawa M, Miyajima N, Tabata S (1998). CyanoBase, a www database containing the complete nucleotide sequence of the genome of Synechocystis sp. strain PCC6803. Nucl Acids Res 26:63-67

Rudi K, Kroken M, Dahlberg OJ, Deggerdal A, Jakobsen KS, Larsen F (1997). Rapid, universal method to isolate PCR-ready DNA using magnetic beads. Biotechniques 22:506-511

Suguna S, Thangavel C, Marutharavindran CR, Shanmugasundaram S (1996). A non-radioactive method for detection of Tn5 Kanamycin phosphotransferase activity in cyanobacteria. Current Science (Bangalore) 71:11

Takeyama H, Takeda D, Yazawa K, Yamada A, Matsunaga T (1997). Expression of the eicosapentaenoic acid synthesis gene cluster from Shewanella sp. in a transgenic marine cyanobacterium, Synechococcus sp. Microbiol 143(Pt 8):2725-2731

Tateno Y, Fukami-Kobayashi K, Miyazaki S, Sugawara H, Gojobori T (1998). DNA Data Bank of Japan at work on genome sequence data. Nucl Acids Res 26:16-20

Wolk CP (1997) Anabaena sp. strain PCC 7120. In: de Bruijn FJ, Lupski JR, Weinstock GM (eds) Bacterial Genomes: Physical Structure and Analysis. Chapman & Hall, New York

Xu Z, Cao J, Liu X, Qiu G, Li B (1997). A simple and efficient protocol for isolation of high molecular weight DNA from the cyanobacterium Spirulina platensis. Biotechnology Techniques 11:631-632

Elhai J, Vepritskiy A, Muro-Pastor AM, Flores E, Wolk CP (1997). Reduction of conjugal transfer efficiency by three restriction activities of Anabaena sp. strain PCC 7120. J Bacteriol 179:1998-2005

Miyake M, Asada Y (1996). Efficient transformation of a thermophilic cyanobacterium, Synechococcus elongatus. J Mar Biotechnol 4:113-116

RNA and transcription

Asayama M, Kabasawa M, Shirai M (1997). A novel genetic organization: The leuA-rpoD1 locus in the cyanobacterium Microcystis aeruginosa K-81. Biochim Biophys Acta 1350:15-20

Asayama M, Suzuki A, Nozawa S, Yamada A, Tanaka K, Takahashi H, Aida T, Shirai M (1997). A new sigma factor homolog in a cyanobacterium: Cloning, sequencing, and light-responsive transcripts of rpoD2 from Microcystis aeruginosa K-81. Biochim Biophys Acta 1351:31-36

Asayama M, Suzuki H, Sato A, Aida T, Tanaka K, Takahashi H, Shirai M (1996). The rpoD1 gene product is a principal sigma factor of RNA polymerase in Microcystis aeruginosa K-81. J Biochem 120:752-758

Asayama M, Tanaka K, Takahashi H, Sato A, Aida T, Shirai M (1996). Cloning, sequencing and characterization of the gene encoding a principal sigma factor homolog from the cyanobacterium Microcystis aeruginosa K-81. Gene (Amsterdam) 181:213-217

Asayama M, Yamada A, Tanaka K, Takahashi H, Shirai M (1996). A new set of PCR primers for specific detection of the gene encoding the principal sigma factor in cyanobacteria. J Gen Appl Microbiol 42:511-515

Caslake LF, Gruber TM, Bryant DA (1997). Expression of two alternative sigma factors of Synechococcus sp. strain PCC 7002 is modulated by carbon and nitrogen stress. Microbiol 143(Pt 12):3807-3818

Gruber TM, Bryant DA (1998). Characterization of the alternative sigma-factors SigD and SigE in Synechococcus sp. strain PCC 7002. SigE is implicated in transcription of post-exponential-phase-specific genes. Arch Microbiol 169:211-219

Luo XZJ, Stevens SE (1997). Isolation of full-length RNA from a thermophilic cyanobacterium. Biotechniques 23:904-910

Paquin B, Kathe SD, Nierzwicki-Bauer SA, Shub DA (1997). Origin and evolution of group I introns in cyanobacterial tRNA genes. J Bacteriol 179:6798-6806

Rudi K, Jakobsen KS (1997). Cyanobacterial tRNA(Leu)(UAA) group I introns have polyphyletic origin. FEMS Microbiol Lett 156:293-298

Schyns G, Jia L, Coursin T, Tandeau de Marsac N, Houmard J (1998). Promoter recognition by a cyanobacterial RNA polymerase: in vitro studies with the Calothrix sp. PCC 7601 transcriptional factors RcaA and RcaD. Plant Molec Biol 36:649-659

Sugimoto Y, Tanaka K, Masuda S, Takahashi H (1997). The rpoD1 gene of Synechococcus sp. strain PCC 7942 encodes the principal sigma factor of RNA polymerase. J Gen Appl Microbiol 43:17-21

Tanaka K, Tozawa Y, Mochizuki N, Shinozaki K, Nagatani A, Wakasa K, Takahashi H (1997). Characterization of three cDNA species encoding plastid RNA polymerase sigma factors in Arabidopsis thaliana: evidence for the sigma factor heterogeneity in higher plant plastids. FEBS Letters 413:309-313

Tanner MA, Anderson EM, Gutell RR, Cech TR (1997). Mutagenesis and comparative sequence analysis of a base triple joining the two domains of group I ribozymes. RNA 3:1037-1051

Tanner MA, Cech TR (1997). Joining the two domains of a group I ribozyme to form the catalytic core. Science (Washington D C) 275:847-849

Vioque A (1997). The RNase P RNA from cyanobacteria: short tandemly repeated repetitive (STRR) sequences are present within the RNase P RNA gene in heterocyst-forming cyanobacteria. Nucl Acids Res 25:3471-3477

Watanabe T, Sugita M, Sugiura M (1998). Identification of 10Sa RNA (tmRNA) homologues from the cyanobacterium Synechococcus sp. strain PCC6301 and related organisms. Biochim Biophys Acta 1396:97-104

Watanabe T, Sugiura M, Sugita M (1997). A novel small stable RNA, 6Sa RNA, from the cyanobacterium Synechococcus sp. strain PCC6301. FEBS Letters 416:302-306

DNA metabolism and plasmids

Agrawal GK, Asayama M, Shirai M (1997). A novel bend of DNA CIT: Changeable bending-center sites of an intrinsic curvature under temperature conditions. FEMS Microbiol Lett 147:139-145

Cassier-Chauvat C, Poncelet M, Chauvat F (1997). Three insertion sequences from the cyanobacterium Synechocystis PCC6803 support the occurrence of horizontal DNA transfer among bacteria. Gene (Amsterdam) 195:257-266

Gabay C, Lieman-Hurwitz J, Hassidim M, Ronen-Tarazi M, Kaplan A (1998). Modification of topA in Synechococcus sp. PCC 7942 resulted in mutants capable of growing under low but not high concentration of CO2. FEMS Microbiol Lett 159:343-347

Gelfand MS, Koonin EV (1997). Avoidance of palindromic words in bacterial and archaeal genomes: A close connection with restriction enzymes. Nucl Acids Res 25:2430-2439

Ito J, Huang Y, Parekh T (1998). Studies on the cyanobacterial family C DNA polymerase. FEMS Microbiol Lett 158:39-43

Meiss G, Franke I, Gimadutdinow O, Urbanke C, Pingoud A (1998). Biochemical characterization of Anabaena sp. strain PCC 7120 non-specific nuclease NucA and its inhibitor NuiA. Eur J Biochem 251:924-934

Mrazek J, Karlin S (1998). Strand compositional asymmetry in bacterial and large viral genomes. Proc Natl Acad Sci USA 95:3720-3725

Muro-Pastor AM, Herrero A, Flores E (1997). The nuiA gene from Anabaena sp. encoding an inhibitor of the NucA sugar-non-specific nuclease. J Mol Biol 268:589-598

Richter S, Hess WR, Krause M, Messer W (1998). Unique organization of the dnaA region from Prochlorococcus marinus CCMP1375, a marine cyanobacterium. Mol Gen Genet 257:534-541

Robinson PJ, Cranenburgh RM, Head IM, Robinson NJ (1997). HIP1 propagates in cyanobacterial DNA via nucleotide substitutions but promotes excision at similar frequencies in Escherichia coli and Synechococcus PCC 7942. Mol Microbiol 24:181-189

Schyns G, Rippka R, Namane A, Campbell D, Herdman M, Houmard J (1997). Prochlorothrix hollandica PCC 9006: Genomic properties of an axenic representative of the chlorophyll a/b-containing oxyphotobacteria. Res Microbiol 148:345-354

Takahashi I, Hayano D, Asayama M, Masahiro F, Watahiki M, Shirai M (1996). Restriction barrier composed of an extracellular nuclease and restriction endonuclease in the unicellular cyanobacterium Microcystis sp. FEMS Microbiol Lett 145:107-111

Tamada T, Kitadokoro K, Higuchi Y, Inaka K, Yasui A, De Ruiter PE, Eker APM, Miki K (1997). Crystal structure of DNA photolyase from Anacystis nidulans. Nature Struct Biol 4:887-891

Veldhuis MJW, Cucci TL, Sieracki ME (1997). Cellular DNA content of marine phytoplankton using two new fluorochromes: Taxonomic and ecological implications. J Phycol 33:527-541

White MA, Bailey JC, Cannon GC, Heinhorst S (1997). Partial purification and characterization of the DNA polymerase from the cyanelles of Cyanophora paradoxa. FEBS Letters 410:509-514

Cox R, Mirkin SM (1997). Characteristic enrichment of DNA repeats in different genomes. Proc Natl Acad Sci USA 94:5237-5242

Xu W, McFadden BA (1997). Sequence analysis of plasmid pCC5.2 from cyanobacterium Synechocystis PCC 6803 that replicates by a rolling circle mechanism. Plasmid 37:95-104

Protein metabolism, folding, and transport

Baier K, Nicklisch S, Maldener I, Lockau W (1996). Evidence for propeptide-assisted folding of the calcium-dependent protease of the cyanobacterium Anabaena. Eur J Biochem 241:750-755

Barbrook AC, Packer JCL, Howe CJ (1996). Inhibition by penem of processing peptidases from cyanobacteria and chloroplast thylakoids. FEBS Letters 398:198-200

Brink S, Bogsch EG, Mant A, Robinson C (1997). Unusual characteristics of amino-terminal and hydrophobic domains in nuclear-encoded thylakoid signal peptides. Eur J Biochem 245:340-348

Glatz A, Horvath I, Varvasovszki V, Kovacs E, Torok Z, Vigh L (1997). Chaperonin genes of the Synechocystis PCC 6803 are differentially regulated under light-dark transition during heat stress. Biochem Biophys Res Commun 239:291-297

Gorbalenya AE (1998). Non-canonical inteins. Nucl Acids Res 26:1741-1748

Hirosawa M, Sazuka T, Yada T (1997). Prediction of translation initiation sites on the genome of Synechocystis sp. strain PCC6803 by Hidden Markov model. DNA Res 4:179-184

Ichetovkin IE, Abramochkin G, Shrader TE (1997). Substrate recognition by the leucyl/phenylalanyl-tRNA-protein transferase. Conservation within the enzyme family and localization to the trypsin-resistant domain. J Biol Chem 272:33009-33014

Lee BH, Hibino T, Jo J, Viale AM, Takabe T (1997). Isolation and characterization of a dnaK genomic locus in a halotolerant cyanobacterium Aphanothece halophytica. Plant Molec Biol 35:763-775

Liu XQ, Hu Z (1997). Identification and characterization of a cyanobacterial DnaX intein. FEBS Letters 408:311-314

Mazel D, Coic E, Blanchard S, Saurin W, Marliere P (1997). A survey of polypeptide deformylase function throughout the eubacterial lineage. J Mol Biol 266:939-949

Nimura K, Yoshikawa H, Takahashi H (1996). DnaK3, one of the three DnaK proteins of cyanobacterium Synechococcus sp. PCC7942, is quantitatively detected in the thylakoid membrane. Biochem Biophys Res Commun 229:334-340

Sazuka T, Ohara O (1997). Towards a proteome project of cyanobacterium Synechocystis sp. strain PCC6803: linking 130 protein spots with their respective genes. Electrophoresis 18:1252-1258

Shi L, Carmichael WW (1997). pp1-cyano2, a protein serine/threonine phosphatase 1 gene from the cyanobacterium Microcystis aeruginosa UTEX 2063. Arch Microbiol 168:528-531

Yada T, Sazuka T, Hirosawa M (1997). Analysis of sequence patterns surrounding the translation initiation sites on Cyanobacterium genome using the hidden Markov model. DNA Res 4:1-7

Zhao RH, Zhang XK, Miao YG, Li LR (1996). Distribution and some properties of chloroplast chaperonin in some algae. Acta Phytophysiologica Sinica 22:237-242 (Chinese)


Sarma TA, Kaur B (1997). Characterization of host-range mutants of cyanophage N-1. Acta Virologica 41:245-250

Sode K, Oonari R, Oozeki M (1997). Induction of a temperate marine cyanophage by heavy metal. J Mar Biotechnol 5:178-180

Wilson WH, Mann NH (1997). Lysogenic and lytic viral production in marine microbial communities. Aquatic Microb Ecol 13:95-100