Extreme sensory complexity encoded in the 10-megabase draft genome sequence of the chromatically acclimating cyanobacterium Tolypothrix sp. PCC 7601

Genome Announcements

Volumn 3, Issue 3, 2015, Pages

  Yerrapragada, Shaila ^a,e   Shukla, Animesh ^b,g   Hallsworth Pepin, Kymberlie ^c   Choi, Kwangmin ^d,h   Wollam, Aye ^c   Clifton, Sandra ^c   Qin, Xiang ^a   Muzny, Donna ^a   Raghuraman, Sriram ^b,d,i   Ashki, Haleh ^b,d,j   Uzman, Akif ^e   Highlander, Sarah K ^a,k   Fryszczyn, Bartlomiej G ^e,l   Fox, George E ^f   Tirumalai, Madhan R ^f   Liu, Yamei ^f,m   Kim, Sun ^d,n   Kehoe, David M ^b   Weinstock, George M ^a,o  

^a BAYLOR COLLEGE OF MEDICINE   (United States)

^b INDIANA UNIVERSITY   (United States)

^c WASHINGTON UNIVERSITY   (United States)

^d INDIANA UNIVERSITY   (United States)

^e UNIVERSITY OF HOUSTON DOWNTOWN   (United States)

^f University of Houston   (United States)

^g NATIONAL CANCER INSTITUTE   (United States)

^h CINCINNATI CHILDREN'S HOSPITAL MEDICAL CENTER   (United States)

ⁱ SIGMA Integrated Reservoir Solutions LLC   (United States)

^j FLORIDA STATE UNIVERSITY   (United States)

^k J CRAIG VENTER INSTITUTE   (United States)

^l Jiangsu Academy of Agricultural Sciences ^*  (United States)

^m INSTITUTE OF PLANT PROTECTION   (China)

ⁿ Seoul National University   (South Korea)

^o JACKSON LABORATORY   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84978970867     PISSN: None     EISSN: 21698287     Source Type: Journal    
DOI: 10.1128/genomeA.00355-15     Document Type: Article

References (18)

1. Grossman AR, Schaefer M, Chiang G, Collier J. 1994. The responses of cyanobacteria to environmental conditions: light and nutrients, p 641-675. In Bryant D (ed), The molecular biology of Cyanobacteria. Kluwer Academic Publishers, Dordrecht, Netherlands.
2. Kehoe DM, Gutu A. 2006. Responding to color: the regulation of complementary chromatic adaptation. Annu Rev Plant Biol 57:127-150. http://dx.doi.org/10.1146/annurev.arplant.57.032905.105215.
3. Tandeau de Marsac N. 1983. Phycobilisomes and complementary chromatic adaptation in cyanobacteria. Bull Inst Pasteur 81:201-254.
4. Grossman AR. 2003. A molecular understanding of complementary chromatic adaptation. Photosynth Res 76:207-215. http://dx.doi.org/10.1023/A:1024907330878.
5. Mazel D, Marlière P. 1989. Adaptive eradication of methionine and cysteine from cyanobacterial light-harvesting proteins. Nature 341:245-248. http://dx.doi.org/10.1038/341245a0.
6. Gutu A, Alvey RM, Bashour S, Zingg D, Kehoe DM. 2011. Sulfatedriven elemental sparing is regulated at the transcriptional and posttranscriptional levels in a filamentous cyanobacterium. J Bacteriol 193: 1449-1460. http://dx.doi.org/10.1128/JB.00885-10.
7. Tandeau de Marsac N, Houmard J. 1993. Adaptation of cyanobacteria to environmental stimuli: new steps towards molecular mechanisms. FEMS Microbiol Rev 104:119-189. http://dx.doi.org/10.1111/j.1574-6968.1993.tb05866.x.
8. Cobley JG, Zerweck E, Reyes R, Mody A, Seludo-Unson JR, Jaeger H, Weerasuriya S, Navankasattusas S. 1993. Construction of shuttle plasmids which can be efficiently mobilized from Escherichia coli into the chromatically adapting cyanobacterium, Fremyella diplosiphon. Plasmid 30:90-105. http://dx.doi.org/10.1006/plas.1993.1037.
9. Quackenbush J, Liang F, Holt I, Pertea G, Upton J. 2000. The TIGR Gene indices: reconstruction and representation of expressed gene sequences. Nucleic Acids Res 28:141-145. http://dx.doi.org/10.1093/nar/28.1.141.
10. Borodovsky M, Mills R, Besemer J, Lomsadze A. 2003. Prokaryotic gene prediction using GeneMark and GeneMark.hmm. Curr Protoc Bioinformatics. Unit 4.5. http://dx.doi.org/10.1002/0471250953.bi0405s01.
11. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL. 1999. Improved microbial gene identification with GLIMMER. Nucleic Acids Res 27: 4636-4641. http://dx.doi.org/10.1093/nar/27.23.4636.
12. Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL, Bateman A. 2008. The Pfam protein families database. Nucleic Acids Res 36:D281-D288. http://dx.doi.org/10.1093/nar/gkm960.
13. Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25: 955-964. http://dx.doi.org/10.1093/nar/25.5.0955.
14. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, Ussery DW. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35:3100-3108. http://dx.doi.org/10.1093/nar/gkm160.
15. Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, Bateman A. 2005. Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res 33:D121-D124. http://dx.doi.org/10.1093/nar/gki081.
16. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M. 2004. The KEGG resource for deciphering the genome. Nucleic Acids Res 32: D277-D280. http://dx.doi.org/10.1093/nar/gkh063.
17. Yu NY, Wagner JR, Laird MR, Melli G, Rey S, Lo R, Dao P, Sahinalp SC, Ester M, Foster LJ, Brinkman FS. 2010. PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics 26:1608-1615. http://dx.doi.org/10.1093/bioinformatics/btq249.
18. Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R. 2005. InterProScan: protein domains identifier. Nucleic Acids Res 33:W116-W120. http://dx.doi.org/10.1093/nar/gki442.