A Database of Plastid Protein Families from Red Algae and Apicomplexa and Expression Regulation of the MoeB Gene

Overview

Journal Biomed Res Int

Publisher Wiley

Specialties Biomedical Engineering
Biotechnology
General Medicine

Date 2015 Jun 27

PMID 26114108

Citations 6

Authors

Oleg A Zverkov

Alexandr V Seliverstov

Vassily A Lyubetsky

Affiliations

Soon will be listed here.

Abstract

We report the database of plastid protein families from red algae, secondary and tertiary rhodophyte-derived plastids, and Apicomplexa constructed with the novel method to infer orthology. The families contain proteins with maximal sequence similarity and minimal paralogous content. The database contains 6509 protein entries, 513 families and 278 nonsingletons (from which 230 are paralog-free, and among the remaining 48, 46 contain at maximum two proteins per species, and 2 contain at maximum three proteins per species). The method is compared with other approaches. Expression regulation of the moeB gene is studied using this database and the model of RNA polymerase competition. An analogous database obtained for green algae and their symbiotic descendants, and applications based on it are published earlier.

Citing Articles

Bioinformatics Screening of Genes Specific for Well-Regenerating Vertebrates Reveals c-answer, a Regulator of Brain Development and Regeneration.

Korotkova D, Lyubetsky V, Ivanova A, Rubanov L, Seliverstov A, Zverkov O Cell Rep. 2019; 29(4):1027-1040.e6.

PMID: 31644900 PMC: 6871517. DOI: 10.1016/j.celrep.2019.09.038.

Highly Conserved Elements and Chromosome Structure Evolution in Mitochondrial Genomes in Ciliates.

Gershgorin R, Gorbunov K, Zverkov O, Rubanov L, Seliverstov A, Lyubetsky V Life (Basel). 2017; 7(1).

PMID: 28264444 PMC: 5370409. DOI: 10.3390/life7010009.

Molecular Phylogenetics 2016.

Lyubetsky V, Piel W, Stadler P Biomed Res Int. 2017; 2016:9029306.

PMID: 28127550 PMC: 5227124. DOI: 10.1155/2016/9029306.

A method for identification of highly conserved elements and evolutionary analysis of superphylum Alveolata.

Rubanov L, Seliverstov A, Zverkov O, Lyubetsky V BMC Bioinformatics. 2016; 17:385.

PMID: 27645252 PMC: 5028923. DOI: 10.1186/s12859-016-1257-5.

Regulation of Expression and Evolution of Genes in Plastids of Rhodophytic Branch.

Zverkov O, Seliverstov A, Lyubetsky V Life (Basel). 2016; 6(1).

PMID: 26840333 PMC: 4810238. DOI: 10.3390/life6010007.

References

van Dongen S, Abreu-Goodger C . Using MCL to extract clusters from networks. Methods Mol Biol. 2011; 804:281-95. DOI: 10.1007/978-1-61779-361-5_15. View

Punta M, Coggill P, Eberhardt R, Mistry J, Tate J, Boursnell C . The Pfam protein families database. Nucleic Acids Res. 2011; 40(Database issue):D290-301. PMC: 3245129. DOI: 10.1093/nar/gkr1065. View

Lyubetsky V, Zverkov O, Rubanov L, Seliverstov A . Modeling RNA polymerase competition: the effect of σ-subunit knockout and heat shock on gene transcription level. Biol Direct. 2011; 6:3. PMC: 3038987. DOI: 10.1186/1745-6150-6-3. View

Minoda A, Weber A, Tanaka K, Miyagishima S . Nucleus-independent control of the rubisco operon by the plastid-encoded transcription factor Ycf30 in the red alga Cyanidioschyzon merolae. Plant Physiol. 2010; 154(3):1532-40. PMC: 2971626. DOI: 10.1104/pp.110.163188. View

Lyubetsky V, Rubanov L, Seliverstov A . Lack of conservation of bacterial type promoters in plastids of Streptophyta. Biol Direct. 2010; 5:34. PMC: 2881121. DOI: 10.1186/1745-6150-5-34. View

Vilella A, Severin J, Ureta-Vidal A, Heng L, Durbin R, Birney E . EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Res. 2008; 19(2):327-35. PMC: 2652215. DOI: 10.1101/gr.073585.107. View

Bailey T, Boden M, Buske F, Frith M, Grant C, Clementi L . MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 2009; 37(Web Server issue):W202-8. PMC: 2703892. DOI: 10.1093/nar/gkp335. View

Katoh K, Standley D . MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013; 30(4):772-80. PMC: 3603318. DOI: 10.1093/molbev/mst010. View

Ohta N, Matsuzaki M, Misumi O, Miyagishima S, Nozaki H, Tanaka K . Complete sequence and analysis of the plastid genome of the unicellular red alga Cyanidioschyzon merolae. DNA Res. 2003; 10(2):67-77. DOI: 10.1093/dnares/10.2.67. View

10.

Homann A, Link G . DNA-binding and transcription characteristics of three cloned sigma factors from mustard (Sinapis alba L.) suggest overlapping and distinct roles in plastid gene expression. Eur J Biochem. 2003; 270(6):1288-300. DOI: 10.1046/j.1432-1033.2003.03494.x. View

11.

Glockner G, Rosenthal A, Valentin K . The structure and gene repertoire of an ancient red algal plastid genome. J Mol Evol. 2000; 51(4):382-90. DOI: 10.1007/s002390010101. View

12.

Starkenburg S, Kwon K, Jha R, McKay C, Jacobs M, Chertkov O . A pangenomic analysis of the Nannochloropsis organellar genomes reveals novel genetic variations in key metabolic genes. BMC Genomics. 2014; 15:212. PMC: 3999925. DOI: 10.1186/1471-2164-15-212. View

13.

Lyubetsky V, Seliverstov A, Zverkov O . Transcription regulation of plastid genes involved in sulfate transport in Viridiplantae. Biomed Res Int. 2013; 2013:413450. PMC: 3773388. DOI: 10.1155/2013/413450. View

14.

DePriest M, Bhattacharya D, Lopez-Bautista J . The plastid genome of the red macroalga Grateloupia taiwanensis (Halymeniaceae). PLoS One. 2013; 8(7):e68246. PMC: 3716797. DOI: 10.1371/journal.pone.0068246. View

15.

Wang L, Mao Y, Kong F, Li G, Ma F, Zhang B . Complete sequence and analysis of plastid genomes of two economically important red algae: Pyropia haitanensis and Pyropia yezoensis. PLoS One. 2013; 8(5):e65902. PMC: 3667073. DOI: 10.1371/journal.pone.0065902. View

16.

Janouskovec J, Liu S, Martone P, Carre W, Leblanc C, Collen J . Evolution of red algal plastid genomes: ancient architectures, introns, horizontal gene transfer, and taxonomic utility of plastid markers. PLoS One. 2013; 8(3):e59001. PMC: 3607583. DOI: 10.1371/journal.pone.0059001. View

17.

Collen J, Porcel B, Carre W, Ball S, Chaparro C, Tonon T . Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida. Proc Natl Acad Sci U S A. 2013; 110(13):5247-52. PMC: 3612618. DOI: 10.1073/pnas.1221259110. View

18.

Forchhammer K . P(II) signal transducers: novel functional and structural insights. Trends Microbiol. 2008; 16(2):65-72. DOI: 10.1016/j.tim.2007.11.004. View

19.

Lysenko E . Plant sigma factors and their role in plastid transcription. Plant Cell Rep. 2007; 26(7):845-59. DOI: 10.1007/s00299-007-0318-7. View

20.

Wallace I, OSullivan O, Higgins D, Notredame C . M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res. 2006; 34(6):1692-9. PMC: 1410914. DOI: 10.1093/nar/gkl091. View