Evolutionary analysis of phycobiliproteins: implications for their structural and functional relationships.

PubWeight™: 0.82‹?›

🔗 View Article (PMID 16830096)

Published in J Mol Evol on July 07, 2006

Authors

Fangqing Zhao1, Song Qin

Author Affiliations

1: Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.

Articles cited by this

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res (1994) 392.47

PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci (1997) 45.07

Adaptive protein evolution at the Adh locus in Drosophila. Nature (1991) 31.65

Position-based sequence weights. J Mol Biol (1994) 24.41

Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput Appl Biosci (1997) 17.32

Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics (2000) 14.84

Bayes empirical bayes inference of amino acid sites under positive selection. Mol Biol Evol (2005) 11.26

Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics (1998) 11.25

Statistical methods for detecting molecular adaptation. Trends Ecol Evol (2000) 10.10

Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol (2002) 7.21

The statistical analysis of mitochondrial DNA polymorphisms: chi 2 and the problem of small samples. Mol Biol Evol (1989) 4.27

Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics (2004) 4.22

Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins. Protein Eng (1996) 3.00

Correlations among amino acid sites in bHLH protein domains: an information theoretic analysis. Mol Biol Evol (2000) 2.81

A fast and sensitive multiple sequence alignment algorithm. Comput Appl Biosci (1989) 2.66

X-ray crystallographic structure of the light-harvesting biliprotein C-phycocyanin from the thermophilic cyanobacterium Mastigocladus laminosus and its resemblance to globin structures. J Mol Biol (1985) 2.42

Cyanobacterial phycobilisomes J Struct Biol (1998) 2.34

False-positive selection identified by ML-based methods: examples from the Sig1 gene of the diatom Thalassiosira weissflogii and the tax gene of a human T-cell lymphotropic virus. Mol Biol Evol (2004) 1.64

Frequent false detection of positive selection by the likelihood method with branch-site models. Mol Biol Evol (2004) 1.49

Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution. Protein Eng (1997) 1.46

Refined three-dimensional structure of phycoerythrocyanin from the cyanobacterium Mastigocladus laminosus at 2.7 A. J Mol Biol (1990) 1.33

CRASP: a program for analysis of coordinated substitutions in multiple alignments of protein sequences. Nucleic Acids Res (2004) 1.32

Evolution of the phycobiliproteins. J Mol Biol (1995) 1.30

Isolation, crystallization, crystal structure analysis and refinement of allophycocyanin from the cyanobacterium Spirulina platensis at 2.3 A resolution. J Mol Biol (1995) 1.30

Structural analysis at 2.2 A of orthorhombic crystals presents the asymmetry of the allophycocyanin-linker complex, AP.LC7.8, from phycobilisomes of Mastigocladus laminosus. Proc Natl Acad Sci U S A (1999) 1.27

Isolation, crystallization, crystal structure analysis and refinement of B-phycoerythrin from the red alga Porphyridium sordidum at 2.2 A resolution. J Mol Biol (1992) 1.26

The 1.45 A three-dimensional structure of C-phycocyanin from the thermophilic cyanobacterium Synechococcus elongatus. J Struct Biol (2003) 1.12

Finding important sites in protein sequences. Proc Natl Acad Sci U S A (2002) 1.05

Developing a structure-function model for the cryptophyte phycoerythrin 545 using ultrahigh resolution crystallography and ultrafast laser spectroscopy. J Mol Biol (2004) 1.04

An algorithm for detecting directional and non-directional positive selection, neutrality and negative selection in protein coding DNA sequences. Gene (2002) 0.98

Crystal structure of C-phycocyanin from Cyanidium caldarium provides a new perspective on phycobilisome assembly. Biophys J (1999) 0.93

Crystal structure of a light-harvesting protein C-phycocyanin from Spirulina platensis. Biochem Biophys Res Commun (2001) 0.91

Structure of the genes encoding the rod-core linker polypeptides of Mastigocladus laminosus phycobilisomes and functional aspects of the phycobiliprotein/linker-polypeptide interactions. Eur J Biochem (1992) 0.88

The crystal structure of a novel unmethylated form of C-phycocyanin, a possible connector between cores and rods in pycobilisomes. J Biol Chem (2003) 0.86

The complete amino acid sequence of R-phycocyanin-I alpha and beta subunits from the red alga Porphyridium cruentum. Structural and phylogenetic relationships of the phycocyanins within the phycobiliprotein families. Eur J Biochem (1994) 0.84

Nobel lecture. A structural basis of light energy and electron transfer in biology. EMBO J (1989) 0.79

Significance of a two-domain structure in subunits of phycobiliproteins revealed by the normal mode analysis. Biophys J (2000) 0.78

Structural-functional analysis of the oligomeric protein R-phycoerythrin. Biol Res (2004) 0.75

Transfer of excitation energy in photosynthesis: some thoughts. Photosynth Res (1989) 0.75

Articles by these authors

Microglial migration mediated by ATP-induced ATP release from lysosomes. Cell Res (2012) 1.25

Roles of microRNA in plant defense and virus offense interaction. Plant Cell Rep (2008) 1.05

Ubiquitylation-independent degradation of Xeroderma pigmentosum group C protein is required for efficient nucleotide excision repair. Nucleic Acids Res (2007) 1.03

Palladium(II)-catalyzed oxidative C-H/C-H cross-coupling of heteroarenes. J Am Chem Soc (2010) 1.00

Increased p75(NTR) expression in hippocampal neurons containing hyperphosphorylated tau in Alzheimer patients. Exp Neurol (2002) 0.99

The p38 mitogen-activated protein kinase augments nucleotide excision repair by mediating DDB2 degradation and chromatin relaxation. J Biol Chem (2008) 0.99

Olfactory identification and apolipoprotein E epsilon 4 allele in mild cognitive impairment. Brain Res (2002) 0.96

Chandrananimycins A approximately C: production of novel anticancer antibiotics from a marine Actinomadura sp. isolate M048 by variation of medium composition and growth conditions. J Antibiot (Tokyo) (2003) 0.96

Chinikomycins A and B: isolation, structure elucidation, and biological activity of novel antibiotics from a marine Streptomyces sp. isolate M045. J Nat Prod (2005) 0.95

N-carboxamido-staurosporine and selina-4(14),7(11)-diene-8,9-diol, new metabolites from a marine Streptomyces sp. J Antibiot (Tokyo) (2006) 0.94

Carotenoid biosynthesis in cyanobacteria: structural and evolutionary scenarios based on comparative genomics. Int J Biol Sci (2006) 0.94

Genome-wide analysis of restriction-modification system in unicellular and filamentous cyanobacteria. Physiol Genomics (2005) 0.94

The nuclear receptor TLX is required for gliomagenesis within the adult neurogenic niche. Mol Cell Biol (2012) 0.93

Thermogravimetric and kinetic analysis of Spirulina wastes under nitrogen and air atmospheres. Bioresour Technol (2013) 0.91

T-muurolol sesquiterpenes from the marine Streptomyces sp. M491 and revision of the configuration of previously reported amorphanes. J Nat Prod (2009) 0.90

Lobophorin C and D, new kijanimicin derivatives from a marine sponge-associated actinomycetal strain AZS17. Mar Drugs (2011) 0.90

A new anthracene derivative from marine Streptomyces sp. W007 exhibiting highly and selectively cytotoxic activities. Mar Drugs (2011) 0.90

Establishment of a micro-particle bombardment transformation system for Dunaliella salina. J Microbiol (2005) 0.90

Biorefinery products from the inulin-containing crop Jerusalem artichoke. Biotechnol Lett (2012) 0.90

Draft genome sequence of the marine bacterium Streptomyces griseoaurantiacus M045, which produces novel manumycin-type antibiotics with a pABA core component. J Bacteriol (2011) 0.89

Genetic and marine cyclonic eddy analyses on the largest macroalgal bloom in the world. Environ Sci Technol (2011) 0.89

Genome-wide comparative analysis of metacaspases in unicellular and filamentous cyanobacteria. BMC Genomics (2010) 0.88

Decreased estrogen receptor-alpha expression in hippocampal neurons in relation to hyperphosphorylated tau in Alzheimer patients. Acta Neuropathol (2003) 0.88

Genome-wide survey of putative serine/threonine protein kinases in cyanobacteria. BMC Genomics (2007) 0.87

Evidence for positive Darwinian selection of Vip gene in Bacillus thuringiensis. J Genet Genomics (2007) 0.86

Phycobilisomes linker family in cyanobacterial genomes: divergence and evolution. Int J Biol Sci (2007) 0.86

Hypolipidemic and antioxidant properties of a polysaccharide fraction from Enteromorpha prolifera. Int J Biol Macromol (2013) 0.85

Age-related spatial cognitive impairment is correlated with increase of synaptotagmin 1 in dorsal hippocampus in SAMP8 mice. Neurobiol Aging (2006) 0.84

Amorphane sesquiterpenes from a marine Streptomyces sp. J Nat Prod (2007) 0.84

Combinational biosynthesis of a fluorescent cyanobacterial holo-alpha-phycocyanin in Escherichia coli by using one expression vector. Appl Biochem Biotechnol (2007) 0.83

Role of Claspin in regulation of nucleotide excision repair factor DDB2. DNA Repair (Amst) (2006) 0.83

Genomic sequence-based discovery of novel angucyclinone antibiotics from marine Streptomyces sp. W007. FEMS Microbiol Lett (2012) 0.82

Intergeneric conjugation in holomycin-producing marine Streptomyces sp. strain M095. Microbiol Res (2006) 0.82

Fatty acid biosynthesis in eukaryotic photosynthetic microalgae: identification of a microsomal delta 12 desaturase in Chlamydomonas reinhardtii. J Microbiol (2008) 0.82

Comparative molecular population genetics of phycoerythrin locus in Prochlorococcus. Genetica (2006) 0.82

Recombinant expression of rt-PA gene (encoding Reteplase) in gametophytes of the seaweed Laminaria japonica (Laminariales, Phaeophyta). Sci China C Life Sci (2008) 0.82

Antioxidant properties of recombinant allophycocyanin expressed in Escherichia coli. J Photochem Photobiol B (2006) 0.82

Kiamycin, a unique cytotoxic angucyclinone derivative from a marine Streptomyces sp. Mar Drugs (2012) 0.81

Inhibitory effect of total flavone of Abelmoschus manihot L. Medic on NMDA receptor-mediated current in cultured rat hippocampal neurons. Neurosci Res (2006) 0.81

Adaptive evolution of cry genes in Bacillus thuringiensis: implications for their specificity determination. Genomics Proteomics Bioinformatics (2007) 0.81

Cloning and characterization of beta-carotene ketolase gene promoter in Haematococcus pluvialis. Acta Biochim Biophys Sin (Shanghai) (2005) 0.81

The protective effect of C-phycocyanin on paraquat-induced acute lung injury in rats. Environ Toxicol Pharmacol (2011) 0.80

Identification and characterization of an intracellular Cu, Zn-superoxide dismutase (icCu/Zn-SOD) gene from clam Venerupis philippinarum. Fish Shellfish Immunol (2009) 0.80

Methyl jasmonate- or gibberellins A3-induced astaxanthin accumulation is associated with up-regulation of transcription of beta-carotene ketolase genes (bkts) in microalga Haematococcus pluvialis. Bioresour Technol (2010) 0.80

Comparative analysis of fatty acid desaturases in cyanobacterial genomes. Comp Funct Genomics (2008) 0.80

Pilot-scale fermentation and purification of the recombinant allophycocyanin over-expressed in Escherichia coli. Biotechnol Lett (2005) 0.80

Imidazolium-functionalized BINOL as a multifunctional receptor for chromogenic and chiral anion recognition. Org Lett (2009) 0.80

Hypoglycemic Properties of Oxovanadium (IV) Coordination Compounds with Carboxymethyl-Carrageenan and Carboxymethyl-Chitosan in Alloxan-Induced Diabetic Mice. Evid Based Complement Alternat Med (2011) 0.79

Functional biosynthesis of an allophycocyan beta subunit in Escherichia coli. J Biosci Bioeng (2009) 0.79

Comparison of envelope-related genes in unicellular and filamentous cyanobacteria. Comp Funct Genomics (2007) 0.79

Functional characterization of sll0659 from Synechocystis sp. PCC 6803. Indian J Biochem Biophys (2008) 0.79

Simultaneous determination and pharmacokinetics of five bufadienolides in rat plasma after oral administration of Chansu extract by SPE-HPLC method. J Pharm Biomed Anal (2007) 0.79

Genome-wide analysis of putative peroxiredoxin in unicellular and filamentous cyanobacteria. BMC Evol Biol (2012) 0.79

Identification of two small heat shock proteins with different response profile to cadmium and pathogen stresses in Venerupis philippinarum. Cell Stress Chaperones (2010) 0.79

Biosynthesis of fluorescent allophycocyanin alpha-subunits by autocatalysis in Escherichia coli. Biotechnol Appl Biochem (2009) 0.79

Molecular cloning and stress-dependent expression of a gene encoding Delta(12)-fatty acid desaturase in the Antarctic microalga Chlorella vulgaris NJ-7. Extremophiles (2009) 0.79

Serine/threonine protein kinase SpkG is a candidate for high salt resistance in the unicellular cyanobacterium Synechocystis sp. PCC 6803. PLoS One (2011) 0.78

Recombination and heterologous expression of allophycocyanin gene in the chloroplast of Chlamydomonas reinhardtii. Acta Biochim Biophys Sin (Shanghai) (2005) 0.78

Completely OH-selective FeCl3-catalyzed Prins cyclization: highly stereoselective synthesis of 4-OH-tetrahydropyrans. J Am Chem Soc (2012) 0.78

Cloning and characterization of allograft inflammatory factor-1 (AIF-1) from Manila clam Venerupis philippinarum. Fish Shellfish Immunol (2010) 0.78

Vertical distribution of bacterial and archaeal communities along discrete layers of a deep-sea cold sediment sample at the East Pacific Rise (approximately 13 degrees N). Extremophiles (2008) 0.78

Computational investigation on the mechanism and the stereoselectivity of Morita-Baylis-Hillman reaction and the effect of the bifunctional catalyst N-methylprolinol. Org Biomol Chem (2010) 0.78

Biosynthesis of fluorescent cyanobacterial allophycocyanin trimer in Escherichia coli. Photosynth Res (2010) 0.78

Isolation and characterization of a stress-dependent plastidial delta12 fatty acid desaturase from the Antarctic microalga Chlorella vulgaris NJ-7. Lipids (2010) 0.78

Isolation, antimicrobial activity, and metabolites of fungus Cladosporium sp. associated with red alga Porphyra yezoensis. Curr Microbiol (2008) 0.78

New electrophilic addition of α-diazoesters with ketones for enantioselective C-N bond formation. J Am Chem Soc (2011) 0.78

Iron-mediated direct Suzuki-Miyaura reaction: a new method for the ortho-arylation of pyrrole and pyridine. Org Lett (2010) 0.77

Identification of archaeon-producing hyperthermophilic alpha-amylase and characterization of the alpha-amylase. Appl Microbiol Biotechnol (2008) 0.77

Genomewide analysis of carotenoid cleavage dioxygenases in unicellular and filamentous cyanobacteria. Comp Funct Genomics (2012) 0.77

A lipase with broad solvent stability from Burkholderia cepacia RQ3: isolation, characteristics and application for chiral resolution of 1-phenylethanol. Bioprocess Biosyst Eng (2016) 0.77

The first molluscan TCTP in Venerupis philippinarum: molecular cloning and expression analysis. Fish Shellfish Immunol (2010) 0.77

The coevolution of phycobilisomes: molecular structure adapting to functional evolution. Comp Funct Genomics (2011) 0.77

Combinational biosynthesis of phycocyanobilin using genetically-engineered Escherichia coli. Biotechnol Lett (2013) 0.76

attB site disruption in marine Actinomyces sp. M048 via DNA transformation of a site-specific integration vector. Biotechnol Appl Biochem (2008) 0.76

Combinational biosynthesis of a fluorescent cyanobacterial holo-alpha-allophycocyanin in Escherichia coli. Biotechnol Lett (2008) 0.76

Effects of iron on fatty acid and astaxanthin accumulation in mixotrophic Chromochloris zofingiensis. Biotechnol Lett (2012) 0.76

Impacts of mariculture on the diversity of bacterial communities within intertidal sediments in the Northeast of China. Microb Ecol (2013) 0.76

Asymmetric total synthesis of onoseriolide, bolivianine, and isobolivianine. Chemistry (2014) 0.75

Biosynthesis and immobilization of biofunctional allophycocyanin. Evid Based Complement Alternat Med (2011) 0.75

Pyrolytic Characteristics and Kinetics of Phragmites australis. Evid Based Complement Alternat Med (2011) 0.75

[Experimental study on the therapeutic effect of C-phycocyanin against pulmonary fibrosis induced by paraquat in rats]. Zhonghua Lao Dong Wei Sheng Zhi Ye Bing Za Zhi (2012) 0.75

Bispuupehenone from the South Chinese Sea sponge Dysidea sp. Acta Crystallogr Sect E Struct Rep Online (2008) 0.75

Evolutionary origins, molecular cloning and expression of carotenoid hydroxylases in eukaryotic photosynthetic algae. BMC Genomics (2013) 0.75

[A simple and controllable method for reproduction of a model of high oxygen tension induced acute lung injury]. Zhonghua Wei Zhong Bing Ji Jiu Yi Xue (2016) 0.75

Optimal light regime for the cultivation of transgenic Laminaria japonica gametophytes in a bubble-column bioreactor. Biotechnol Lett (2005) 0.75

[HPLC-ELSD fingerprint of Marsdenia tenacissima from different habitats]. Zhongguo Zhong Yao Za Zhi (2012) 0.75

Hualyzin, a symmetrical urea derivative isolated from Penicillium herquei isolate GA4. J Nat Prod (2008) 0.75

[Screening type II alveolar epithelial cell apoptosis related microRNA]. Zhonghua Wei Zhong Bing Ji Jiu Yi Xue (2013) 0.75

Theoretical study on the gas-phase reaction mechanism between nickel monoxide and methane for syngas production. J Comput Chem (2009) 0.75

[Relationship between tumorous stem mustard yield and soil fertility in Fuling, Southwest China]. Ying Yong Sheng Tai Xue Bao (2013) 0.75

[Microbial diversity of sediments from the coasts of Dalian Changshan Islands]. Wei Sheng Wu Xue Bao (2011) 0.75

Cloning, expression and characterization of phycoerythrin gene from Ceramium boydenn. DNA Seq (2006) 0.75

Suspension culture of gametophytes of transgenic kelp in a photobioreactor. Biotechnol Lett (2005) 0.75

Gene cloning, sequence analysis, and expression profiles of a novel β-ring carotenoid hydroxylase gene from the photoheterotrophic green alga Chlorella kessleri. Mol Biol Rep (2014) 0.75

An entry to vinylcyclopropane through palladium-catalyzed intramolecular cyclopropanation of alkenes with unstabilized allylic tosylhydrazones. Chem Commun (Camb) (2015) 0.75

Biosynthesis of a stable allophycocyanin beta subunit in metabolically engineered Escherichia coli. J Biosci Bioeng (2012) 0.75

Unstable-Fe-site-induced formation of mesopores in microporous zeolite Y without using organic templates. Chem Commun (Camb) (2014) 0.75

Purification of 6×His-tagged phycobiliprotein using zinc-decorated silica-coated magnetic nanoparticles. J Chromatogr B Analyt Technol Biomed Life Sci (2011) 0.75

Degradation mechanism of Methyl Orange by electrochemical process on RuO(x)-PdO/Ti electrode. Water Sci Technol (2011) 0.75