Molecular and genetic analyses of Tic20 homologues in Arabidopsis thaliana chloroplasts

The Tic20 protein was identified in pea (Pisum sativum) as a component of the chloroplast protein import apparatus. In Arabidopsis, there are four Tic20 homologues, termed atTic20‐I, atTic20‐IV, atTic20‐II and atTic20‐V, all with predicted topological similarity to the pea protein (psTic20). Analysis of Tic20 sequences from many species indicated that they are phylogenetically unrelated to mitochondrial Tim17‐22‐23 proteins, and that they form two evolutionarily conserved subgroups [characterized by psTic20/atTic20‐I/IV (Group 1) and atTic20‐II/V (Group 2)]. Like psTic20, all four Arabidopsis proteins have a predicted transit peptide consistent with targeting to the inner envelope. Envelope localization of each one was confirmed by analysis of YFP fusions. RT‐PCR and microarray data revealed that the four genes are expressed throughout development. To assess the functional significance of the genes, T‐DNA mutants were identified. Homozygous tic20‐I plants had an albino phenotype that correlated with abnormal chloroplast development and reduced levels of chloroplast proteins. However, knockouts for the other three genes were indistinguishable from the wild type. To test for redundancy, double and triple mutants were studied; apart from those involving tic20‐I, none was distinguishable from the wild type. The tic20‐I tic20‐II and tic20‐I tic20‐V double mutants were albino, like the corresponding tic20‐I parent. In contrast, tic20‐I tic20‐IV double homozygotes could not be identified, due to gametophytic and embryonic lethality. Redundancy between atTic20‐I and atTic20‐IV was confirmed by complementation analysis. Thus, atTic20‐I and atTic20‐IV are the major functional Tic20 isoforms in Arabidopsis, with partially overlapping roles. While the Group 2 proteins have been conserved over approximately 1.2 billion (1.2 × 10⁹) years, they are not essential for normal development.     

Campylobacter jejuni Lipooligosaccharide Sialylation,Phosphorylation, and Amide/Ester Linkage Modifications Fine-tune Human Toll-like Receptor 4 Activation

Campylobacter jejuni is a leading cause of acute gastroenteritis. C. jejuni lipooligosaccharide (LOS) is a potent activator of Toll-like receptor (TLR) 4-mediated innate immunity. Structural variations of the LOS have been previously reported in the oligosaccharide (OS) moiety, the disaccharide lipid A (LA) backbone, and the phosphorylation of the LA. Here, we studied LOS structural variation between C. jejuni strains associated with different ecological sources and analyzed their ability to activate TLR4 function. MALDI-TOF MS was performed to characterize structural variation in both the OS and LA among 15 different C. jejuni isolates. Cytokine induction in THP-1 cells and primary monocytes was correlated with LOS structural variation in each strain. Additionally, structural variation was correlated with the source of each strain. OS sialylation, increasing abundance of LA d-glucosamine versus 2,3-diamino-2,3-dideoxy-d-glucose, and phosphorylation status all correlated with TLR4 activation as measured in THP-1 cells and monocytes. Importantly, LOS-induced inflammatory responses were similar to those elicited by live bacteria, highlighting the prominent contribution of the LOS component in driving host immunity. OS sialylation status but not LA structure showed significant association with strains clustering with livestock sources. Our study highlights how variations in three structural components of C. jejuni LOS alter TLR4 activation and consequent monocyte activation.     

Preliminary studies of the impact of excreted N on cycling and uptake of N in pasture systems using natural abundance stable isotopic discrimination

The possibility of using natural abundance techniques to determine N transformations and flows after deposition of cattle dung has been examined. These preliminary results showed that ¹⁵N in dung was greater than in plants growing in association with particular pats. This, and other observational information, indicated that dung pats of different ages were being examined. There were significant variations in plant ¹⁵N signatures within and between species grown in association and away from the dung. It was probable that variation in plant ¹⁵N was brought about by changes in soil mineral N pools after transfer of N derived from the dung. This resulted in different ¹⁵N signatures in Trifolium repens (because of changes in N utilization from soil or atmospheric pools), in Lolium perenne (because of changes in ¹⁵N in soil mineral N), but not in Ranunculus repens (because the majority of active roots were outside the range of immediate influence of the deposited dung). The differences in ¹⁵N allowed the development of hypotheses for changes in soil N pools and the acquisition of N by plants from soil, dung or atmospheric sources.     

Future trends in nitrogen research

N research effort has undergone major changes over recent decades with changing emphasis because of environmental problems and issues. This driving force, coupled with a universal desire to improve N-use efficiency, appreciation of the importance of maintaining soil resource quality and a need to provide integrated landscape managements, will continue to prompt new research areas and issues for study. Already, much information has been provided and new approaches and needs defined. It will be essential in future research to take full note of the many interactions that occur and to provide a mechanistic basis so that scaling of effects can be undertaken with the appropriate simplification without being superficial. Examples of interactions, as well as fundamental gaps in the basic processes are discussed and needs for future research identified.     

Rates of nuclear and cytoplasmic mitochondrial DNA sequence divergence in mammals

Differential rates of nucleotide substitution among different gene segments and between distinct evolutionary lineages is well documented among mitochondrial genes and is likely a consequence of locus-specific selective constraints that delimit mutational divergence over evolutionary time. We compared sequence variation of 18 homologous loci (15 coding genes and 3 parts of the control region) among 10 mammalian mitochondrial DNA genomes which allowed us to describe different mitochondrial evolutionary patterns and to produce an estimation of the relative order of gene divergence. The relative rates of divergence of mitochondrial DNA genes in the family Felidae were estimated by comparing their divergence from homologous counterpart genes included in nuclear mitochondrial DNA (Numt, pronounced "new might"), a genomic fossil that represents an ancient transfer of 7.9 kb of mitochondrial DNA to the nuclear genome of an ancestral species of the domestic cat (Felis catus). Phylogenetic analyses of mitochondrial (mtDNA) sequences with multiple outgroup species were conducted to date the ancestral node common to the Numt and the cytoplasmic (Cymt) mtDNA genes and to calibrate the rate of sequence divergence of mitochondrial genes relative to nuclear homologous counterparts. By setting the fastest substitution rate as strictly mutational, an empirical "selective retardation index" is computed to quantify the sum of all constraints, selective and otherwise, that limit sequence divergence of mitochondrial gene sequences over time.      

Rapid evolution in a conserved gene family. Evolution of the actin gene family in the sea urchin genus Heliocidaris and related genera

Camarodont sea urchins possess a rapidly evolving actin gene family whose members are expressed in distinct cell lineages in a developmentally regulated fashion. Evolutionary changes in the actin gene family of echinoids include alterations in number of family members, site of expression, and gene linkage, and a dichotomy between rapidly and slowly evolving isoform-specific 3' untranslated regions. We present sequence comparisons and an analysis of the actin gene family in two congeneric sea urchins that develop in radically different modes, Heliocidaris erythrogramma and H. tuberculata. The sequences of several actin genes from the related species Lytechinus variegatus are also presented. We compare the features of the Heliocidaris and Lytechinus actin genes to those of the the actin gene families of other closely related sea urchins and discuss the nature of the evolutionary changes among sea urchin actins and their relationship to developmental mode.      

The apportionment of dinucleotide repeat diversity in Native Americans and Europeans: a new approach to measuring gene identity reveals asymmetric patterns of divergence

The purpose of this paper is to assess the extent of gene identity and differentiation at 33 dinucleotide repeat loci (377 total alleles) within and among three European and three Native American populations. In order to do this, we show that a maximum-likelihood method proposed for phylogenetic trees (Cavalli-Sforza and Piazza 1975) can be used to estimate gene identity (Nei 1987) with respect to any hierarchical structure. This method allows gene differentiation to be evaluated with respect to any internal node of a hierarchy. It also allows a generalization of F- and G-statistics to situations with unequal expected levels of differentiation. Our principal finding is that levels of genetic differentiation are unique to specific populations and levels of nesting. The populations of European origin show very little internal differentiation; moreover, their continental average is close to the total population defined by the aggregate of Europeans and Native Americans. By contrast, the Native American populations show moderate levels of internal differentiation, and a great distance between their continental average and the total. The results of analyses of subsets of loci that were selected to have high gene diversities in either Europeans or Native Americans closely parallel those from the total set of loci. This suggests that the principal results are unlikely to be caused by a European ascertainment bias in locus selection. In summary, our findings demonstrate that partitions of gene diversity into within- and between-populations components are heavily biased by the populations analyzed and the models fitted. Optimistically, however, more information is available to analyze population history and evolution by quantifying, as we have done, the uniqueness of patterns of differentiation.      

Intracellular signalling: the language of the chloroplast

Chloroplasts emit signals that modulate nuclear gene expression, thereby ensuring the proper assembly of the photosynthetic apparatus. Recent studies have provided major new insights into one of these signalling mechanisms, and identified the chlorophyll precursor Mg-protoporphyrin IX as a key signalling molecule.