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

A novel algorithm and original software were used to cluster all proteins encoded in plastids of 72 species of the rhodophytic branch. The results are publicly available at http://lab6.iitp.ru/ppc/redline72/ in a database that allows fast identification of clusters (protein families) both by a fragment of an amino acid sequence and by a phylogenetic profile of a protein. No such integral clustering with the corresponding functions can be found in the public domain. The putative regulons of the transcription factors Ycf28 and Ycf29 encoded in the plastids were identified using the clustering and the database. A regulation of translation initiation was proposed for the ycf24 gene in plastids of certain red algae and apicomplexans as well as a regulation of a putative gene in apicoplasts of Babesia spp. and Theileria parva. The conserved regulation of the ycf24 gene expression and specificity alternation of the transcription factor Ycf28 were shown in the plastids. A phylogenetic tree of plastids was generated for the rhodophytic branch. The hypothesis of the origin of apicoplasts from the common ancestor of all apicomplexans from plastids of red algae was confirmed.

[1]  J. Kruskal.  On the shortest spanning subtree of a graph and the traveling salesman problem , 1956 .

[2]  K. Ohyama,et al.  cemA homologue essential to CO2 transport in the cyanobacterium Synechocystis PCC6803. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[3]  Roderic D. M. Page,et al.  TreeView: an application to display phylogenetic trees on personal computers , 1996, Comput. Appl. Biosci..

[4]  J. Palmer,et al.  A Plastid of Probable Green Algal Origin in Apicomplexan Parasites , 1997, Science.

[5]  J. Keithly,et al.  Cryptosporidium parvum appears to lack a plastid genome. , 2000, Microbiology.

[6]  A. Homann,et al.  DNA-binding and transcription characteristics of three cloned sigma factors from mustard (Sinapis alba L.) suggest overlapping and distinct roles in plastid gene expression. , 2003, European journal of biochemistry.

[7]  Guangli Zhu,et al.  Apicoplast genome of the coccidian Eimeria tenella. , 2003, Gene.

[8]  G. Crooks,et al.  WebLogo: a sequence logo generator. , 2004, Genome research.

[9]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[10]  Jonathan E. Allen,et al.  Genome Sequence of Theileria parva, a Bovine Pathogen That Transforms Lymphocytes , 2005, Science.

[11]  A. Sorokin,et al.  Electrostatic potentials of E.coli genome DNA. , 2005, Journal of biomolecular structure & dynamics.

[12]  A. Bolshoy,et al.  Involvement of DNA curvature in intergenic regions of prokaryotes , 2006, Nucleic acids research.

[13]  Yifan Hu,et al.  Efficient, High-Quality Force-Directed Graph Drawing , 2006 .

[14]  C. Omoto,et al.  Gregarina niphandrodes may Lack Both a Plastid Genome and Organelle , 2007, The Journal of eukaryotic microbiology.

[15]  M. Reith,et al.  Complete nucleotide sequence of thePorphyra purpurea chloroplast genome , 1995, Plant Molecular Biology Reporter.

[16]  Shelby L. Bidwell,et al.  Genome Sequence of Babesia bovis and Comparative Analysis of Apicomplexan Hemoprotozoa , 2007, PLoS pathogens.

[17]  Stijn van Dongen,et al.  Graph Clustering Via a Discrete Uncoupling Process , 2008, SIAM J. Matrix Anal. Appl..

[18]  E. Birney,et al.  Pfam: the protein families database , 2013, Nucleic Acids Res..

[19]  D. Knowles,et al.  Babesia bovis: a comprehensive phylogenetic analysis of plastid-encoded genes supports green algal origin of apicoplasts. , 2009, Experimental parasitology.

[20]  A. Seliverstov,et al.  Analysis of the 5′-leader regions of several plastid genes in protozoa of the phylum apicomplexa and red algae , 2009, Molecular Biology.

[21]  E. A. Lysenko,et al.  Rapid evolution of promoters for the plastome gene ndhF in flowering plants , 2009, Russian Journal of Plant Physiology.

[22]  A. Horák,et al.  A common red algal origin of the apicomplexan, dinoflagellate, and heterokont plastids , 2010, Proceedings of the National Academy of Sciences.

[23]  P. Keeling,et al.  The Complete Plastid Genomes of the Two ‘Dinotoms’ Durinskia baltica and Kryptoperidinium foliaceum , 2010, PloS one.

[24]  A. Weber,et al.  Nucleus-Independent Control of the Rubisco Operon by the Plastid-Encoded Transcription Factor Ycf30 in the Red Alga Cyanidioschyzon merolae1[C][W][OA] , 2010, Plant Physiology.

[25]  V. Lyubetsky,et al.  Lack of conservation of bacterial type promoters in plastids of Streptophyta , 2010, Biology Direct.

[26]  L. Holm,et al.  The Pfam protein families database , 2005, Nucleic Acids Res..

[27]  V. Lyubetsky,et al.  NtcA and NtcB regulons in cyanobacteria and rhodophyta chloroplasts , 2011, Molecular Biology.

[28]  Plastid-encoded protein families specific for narrow taxonomic groups of algae and protozoa , 2012, Molecular Biology.

[29]  I. Igarashi,et al.  Apicoplast-Targeting Antibacterials Inhibit the Growth of Babesia Parasites , 2012, Antimicrobial Agents and Chemotherapy.

[30]  The apicoplast genome of Leucocytozoon caulleryi, a pathogenic apicomplexan parasite of the chicken , 2013, Parasitology Research.

[31]  Koichiro Tamura,et al.  MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. , 2013, Molecular biology and evolution.

[32]  A. Holder,et al.  Correction: The Unique Structure of the Apicoplast Genome of the Rodent Malaria Parasite Plasmodium chabaudi chabaudi , 2013, PLoS ONE.

[33]  V. Lyubetsky,et al.  Transcription Regulation of Plastid Genes Involved in Sulfate Transport in Viridiplantae , 2013, BioMed research international.

[34]  A. Holder,et al.  The Unique Structure of the Apicoplast Genome of the Rodent Malaria Parasite Plasmodium chabaudi chabaudi , 2013, PloS one.

[35]  B. Henrissat,et al.  Genome of the red alga Porphyridium purpureum , 2013, Nature Communications.

[36]  V. Lyubetsky,et al.  Elaboration of the Homologous Plastid-Encoded Protein Families that Separate Paralogs in Magnoliophytes , 2013 .

[37]  J. Lopes,et al.  Compositional Biases among Synonymous Substitutions Cause Conflict between Gene and Protein Trees for Plastid Origins , 2014, Molecular biology and evolution.

[38]  Alexander V. Kel'manov,et al.  A 2-approximate algorithm to solve one problem of the family of disjoint vector subsets , 2014, Autom. Remote. Control..

[39]  A. Kel'manov,et al.  An FPTAS for a vector subset search problem , 2014 .

[40]  Alexandros Stamatakis,et al.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..

[41]  A. Kel'manov,et al.  An approximating polynomial algorithm for a sequence partitioning problem , 2014 .

[42]  C. B. Mamoun,et al.  Sequence and Annotation of the Apicoplast Genome of the Human Pathogen Babesia microti , 2014, PloS one.

[43]  V. Aleoshin,et al.  Ultrastructure and 28S rDNA phylogeny of two gregarines: Cephaloidophora cf. communis and Heliospora cf. longissima with remarks on gregarine morphology and phylogenetic analysis , 2014 .

[44]  Lan He,et al.  Characterization and annotation of Babesia orientalis apicoplast genome , 2015, Parasites & Vectors.

[45]  A. Kel'manov,et al.  A randomized algorithm for two-cluster partition of a set of vectors , 2015 .

[46]  Lori Rowe,et al.  Genetic similarities between Cyclospora cayetanensis and cecum-infecting avian Eimeria spp. in apicoplast and mitochondrial genomes , 2015, Parasites & Vectors.

[47]  J. Lukeš,et al.  The Organellar Genomes of Chromera and Vitrella, the Phototrophic Relatives of Apicomplexan Parasites. , 2015, Annual review of microbiology.

[48]  A. Kel'manov,et al.  An approximation polynomial-time algorithm for a sequence bi-clustering problem , 2015 .

[49]  C. Lane,et al.  The ghost plastid of Choreocolax polysiphoniae , 2015, Journal of phycology.

[50]  V. Lyubetsky,et al.  A Database of Plastid Protein Families from Red Algae and Apicomplexa and Expression Regulation of the moeB Gene , 2015, BioMed research international.