New records and noteworthy data of plants, algae and fungi in SE Europe and adjacent regions, 12

This paper presents new records and noteworthy data on the following taxa in SE Europe and adjacent regions: red algae Hildenbrandia rivularis, saprotrophic fungus Cryptomarasmius corbariensis, lichenised fungi Lecanora stenotropa, Micarea misella and Sticta sylvatica, liverworts Fossombronia caespitiformis and Peltolepis quadrata, mosses Dicranoweisia cirrata and Fissidens exilis, horsetail Equisetum × moorei, gymnosperm Juniperus virginiana, monocots Galanthus reginae-olgae subsp. vernalis and Spiranthes spiralis and dicots Linaria pelisseriana, Parthenocissus quinquefolia, Pilosella rhodopea and Taraxacum erythrospermum are given within SE Europe and adjacent regions

The 3-Base Periodicity and Codon Usage of Coding Sequences Are Correlated with Gene Expression at the Level of Transcription Elongation

Background: Gene transcription is regulated by DNA transcriptional regulatory elements, promoters and enhancers that are located outside the coding regions. Here, we examine the characteristic 3-base periodicity of the coding sequences and analyse its correlation with the genome-wide transcriptional profile of yeast. Principal Findings: The analysis of coding sequences by a new class of indices proposed here identified two different sources of 3-base periodicity: the codon frequency and the codon sequence. In exponentially growing yeast cells, the codon-frequency component of periodicity accounts for 71.9 % of the variability of the cellular mRNA by a strong association with the density of elongating mRNA polymerase II complexes. The mRNA abundance explains most of the correlation between the codon-frequency component of periodicity and protein levels. Furthermore, pyrimidine-ending codons of the four-fold degenerate small amino acids alanine, glycine and valine are associated with genes with double the transcription rate of those associated with purine-ending codons. Conclusions: We demonstrate that the 3-base periodicity of coding sequences is higher than expected by the codon usage frequency (CUF) and that its components, associated with codon bias and amino acid composition, are correlated with gene expression, principally at the level of transcription elongation. This indicates a role of codon sequences in maximising the transcription efficiency in exponentially growing yeast cells. Moreover, the results contrast with the common Darwinia

Large Scale Comparative Codon-Pair Context Analysis Unveils General Rules that Fine-Tune Evolution of mRNA Primary Structure

BACKGROUND: Codon usage and codon-pair context are important gene primary structure features that influence mRNA decoding fidelity. In order to identify general rules that shape codon-pair context and minimize mRNA decoding error, we have carried out a large scale comparative codon-pair context analysis of 119 fully sequenced genomes. METHODOLOGIES/PRINCIPAL FINDINGS: We have developed mathematical and software tools for large scale comparative codon-pair context analysis. These methodologies unveiled general and species specific codon-pair context rules that govern evolution of mRNAs in the 3 domains of life. We show that evolution of bacterial and archeal mRNA primary structure is mainly dependent on constraints imposed by the translational machinery, while in eukaryotes DNA methylation and tri-nucleotide repeats impose strong biases on codon-pair context. CONCLUSIONS: The data highlight fundamental differences between prokaryotic and eukaryotic mRNA decoding rules, which are partially independent of codon usage

Design Parameters to Control Synthetic Gene Expression in Escherichia coli

BACKGROUND:Production of proteins as therapeutic agents, research reagents and molecular tools frequently depends on expression in heterologous hosts. Synthetic genes are increasingly used for protein production because sequence information is easier to obtain than the corresponding physical DNA. Protein-coding sequences are commonly re-designed to enhance expression, but there are no experimentally supported design principles. PRINCIPAL FINDINGS:To identify sequence features that affect protein expression we synthesized and expressed in E. coli two sets of 40 genes encoding two commercially valuable proteins, a DNA polymerase and a single chain antibody. Genes differing only in synonymous codon usage expressed protein at levels ranging from undetectable to 30% of cellular protein. Using partial least squares regression we tested the correlation of protein production levels with parameters that have been reported to affect expression. We found that the amount of protein produced in E. coli was strongly dependent on the codons used to encode a subset of amino acids. Favorable codons were predominantly those read by tRNAs that are most highly charged during amino acid starvation, not codons that are most abundant in highly expressed E. coli proteins. Finally we confirmed the validity of our models by designing, synthesizing and testing new genes using codon biases predicted to perform well. CONCLUSION:The systematic analysis of gene design parameters shown in this study has allowed us to identify codon usage within a gene as a critical determinant of achievable protein expression levels in E. coli. We propose a biochemical basis for this, as well as design algorithms to ensure high protein production from synthetic genes. Replication of this methodology should allow similar design algorithms to be empirically derived for any expression system

New records and noteworthy data of plants, algae and fungi in SE Europe and adjacent regions, 12

This paper presents new records and noteworthy data on the following taxa in SE Europe and adjacent regions: red algae Hildenbrandia rivularis, saprotrophic fungus Cryptomarasmius corbariensis, lichenised fungi Lecanora stenotropa, Micarea misella and Sticta sylvatica, liverworts Fossombronia caespitiformis and Peltolepis quadrata, mosses Dicranoweisia cirrata and Fissidens exilis, horsetail Equisetum × moorei, gymnosperm Juniperus virginiana, monocots Galanthus reginae-olgae subsp. vernalis and Spiranthes spiralis and dicots Linaria pelisseriana, Parthenocissus quinquefolia, Pilosella rhodopea and Taraxacum erythrospermum are given within SE Europe and adjacent regions

Novi i značajni podaci o biljkama, algama i gljivama iz JI Evrope i susednih regiona, 9

This paper presents new records and noteworthy data on the following taxa in SE Europe and adjacent regions: red algae Lemanea fucina and Paralemanea annulata, parasitic fungus Anthracoidea pratensis, saprotrophic fungi Cyathus olla, Massaria campestris, and Xylaria sicula, stonewort Chara canescens, liverworts Gymnomitrion commutatum and Porella baueri, moss Acaulon triquetrum, monocots Anacamptis laxiflora, Cephalanthera damasonium, and Himantoglossum robertianum and dicot Jacobaea othonnae are given within SE Europe and adjacent regions.U radu su prikazani novi i značajni podaci sa područja JI Evrope i susednih regiona o sledećim taksonima: crvenim algama Lemanea fucina i Paralemanea annulata, parazitskoj gljivi Anthracoidea pratensis, saprofitskim gljivama Cyathus olla, Massaria campestris i Xylaria sicula, pršljenčici Chara canescens, jetrenjačama Gymnomitrion commutatum i Porella baueri, mahovini Acaulon triquetrum, monokotilama Anacamptis laxiflora, Cephalanthera damasonium i Himantoglossum robertianum i dikotili Jacobaea othonnae