High Code Density Research Articles

A Rickettsiales symbiont of amoebae with ancient features.

The Rickettsiae comprise intracellular bacterial symbionts and pathogens infecting diverse eukaryotes. Here, we provide a detailed characterization of 'Candidatus Jidaibacter acanthamoeba', a rickettsial symbiont of Acanthamoeba. The bacterium establishes the infection in its amoeba host within 2 h where it replicates within vacuoles. Higher bacterial loads and accelerated spread of infection at elevated temperatures were observed. The infection had a negative impact on host growth rate, although no increased levels of host cell lysis were seen. Phylogenomic analysis identified this bacterium as member of the Midichloriaceae. Its 2.4 Mb genome represents the largest among Rickettsiales and is characterized by a moderate degree of pseudogenization and a high coding density. We found an unusually large number of genes encoding proteins with eukaryotic-like domains such as ankyrins, leucine-rich repeats and tetratricopeptide repeats, which likely function in host interaction. There are a total of three divergent, independently acquired type IV secretion systems, and 35 flagellar genes representing the most complete set found in an obligate intracellular Alphaproteobacterium. The deeply branching phylogenetic position of 'Candidatus Jidaibacter acanthamoeba' together with its ancient features place it closely to the rickettsial ancestor and helps to better understand the transition from a free-living to an intracellular lifestyle.

Genomic and proteomic characterization of “Candidatus Nitrosopelagicus brevis”: An ammonia-oxidizing archaeon from the open ocean

Thaumarchaeota are among the most abundant microbial cells in the ocean, but difficulty in cultivating marine Thaumarchaeota has hindered investigation into the physiological and evolutionary basis of their success. We report here a closed genome assembled from a highly enriched culture of the ammonia-oxidizing pelagic thaumarchaeon CN25, originating from the open ocean. The CN25 genome exhibits strong evidence of genome streamlining, including a 1.23-Mbp genome, a high coding density, and a low number of paralogous genes. Proteomic analysis recovered nearly 70% of the predicted proteins encoded by the genome, demonstrating that a high fraction of the genome is translated. In contrast to other minimal marine microbes that acquire, rather than synthesize, cofactors, CN25 encodes and expresses near-complete biosynthetic pathways for multiple vitamins. Metagenomic fragment recruitment indicated the presence of DNA sequences >90% identical to the CN25 genome throughout the oligotrophic ocean. We propose the provisional name "Candidatus Nitrosopelagicus brevis" str. CN25 for this minimalist marine thaumarchaeon and suggest it as a potential model system for understanding archaeal adaptation to the open ocean.

Insights into the metabolism, lifestyle and putative evolutionary history of the novel archaeal phylum 'Diapherotrites'.

The archaeal phylum 'Diapherotrites' was recently proposed based on phylogenomic analysis of genomes recovered from an underground water seep in an abandoned gold mine (Homestake mine in Lead, SD, USA). Here we present a detailed analysis of the metabolic capabilities and genomic features of three single amplified genomes (SAGs) belonging to the 'Diapherotrites'. The most complete of the SAGs, Candidatus 'Iainarchaeum andersonii' (Cand. IA), had a small genome (∼1.24 Mb), short average gene length (822 bp), one ribosomal RNA operon, high coding density (∼90.4%), high percentage of overlapping genes (27.6%) and low incidence of gene duplication (2.16%). Cand. IA genome possesses limited catabolic capacities that, nevertheless, could theoretically support a free-living lifestyle by channeling a narrow range of substrates such as ribose, polyhydroxybutyrate and several amino acids to acetyl-coenzyme A. On the other hand, Cand. IA possesses relatively well-developed anabolic capabilities, although it remains auxotrophic for several amino acids and cofactors. Phylogenetic analysis suggests that the majority of Cand. IA anabolic genes were acquired from bacterial donors via horizontal gene transfer. We thus propose that members of the 'Diapherotrites' have evolved from an obligate symbiotic ancestor by acquiring anabolic genes from bacteria that enabled independent biosynthesis of biological molecules previously acquired from symbiotic hosts. 'Diapherotrites' 16S rRNA genes exhibit multiple mismatches with the majority of archaeal 16S rRNA primers, a fact that could be responsible for their observed rarity in amplicon-generated data sets. The limited substrate range, complex growth requirements and slow growth rate predicted could be responsible for its refraction to isolation.

Genome Degeneration and Adaptation in a Nascent Stage of Symbiosis

Symbiotic associations between animals and microbes are ubiquitous in nature, with an estimated 15% of all insect species harboring intracellular bacterial symbionts. Most bacterial symbionts share many genomic features including small genomes, nucleotide composition bias, high coding density, and a paucity of mobile DNA, consistent with long-term host association. In this study, we focus on the early stages of genome degeneration in a recently derived insect-bacterial mutualistic intracellular association. We present the complete genome sequence and annotation of Sitophilus oryzae primary endosymbiont (SOPE). We also present the finished genome sequence and annotation of strain HS, a close free-living relative of SOPE and other insect symbionts of the Sodalis-allied clade, whose gene inventory is expected to closely resemble the putative ancestor of this group. Structural, functional, and evolutionary analyses indicate that SOPE has undergone extensive adaptation toward an insect-associated lifestyle in a very short time period. The genome of SOPE is large in size when compared with many ancient bacterial symbionts; however, almost half of the protein-coding genes in SOPE are pseudogenes. There is also evidence for relaxed selection on the remaining intact protein-coding genes. Comparative analyses of the whole-genome sequence of strain HS and SOPE highlight numerous genomic rearrangements, duplications, and deletions facilitated by a recent expansion of insertions sequence elements, some of which appear to have catalyzed adaptive changes. Functional metabolic predictions suggest that SOPE has lost the ability to synthesize several essential amino acids and vitamins. Analyses of the bacterial cell envelope and genes encoding secretion systems suggest that these structures and elements have become simplified in the transition to a mutualistic association.

The Complete Genome Sequence of Thermoproteus tenax: A Physiologically Versatile Member of the Crenarchaeota

Here, we report on the complete genome sequence of the hyperthermophilic Crenarchaeum Thermoproteus tenax (strain Kra1, DSM 2078T) a type strain of the crenarchaeotal order Thermoproteales. Its circular 1.84-megabase genome harbors no extrachromosomal elements and 2,051 open reading frames are identified, covering 90.6% of the complete sequence, which represents a high coding density. Derived from the gene content, T. tenax is a representative member of the Crenarchaeota. The organism is strictly anaerobic and sulfur-dependent with optimal growth at 86°C and pH 5.6. One particular feature is the great metabolic versatility, which is not accompanied by a distinct increase of genome size or information density as compared to other Crenarchaeota. T. tenax is able to grow chemolithoautotrophically (CO2/H2) as well as chemoorganoheterotrophically in presence of various organic substrates. All pathways for synthesizing the 20 proteinogenic amino acids are present. In addition, two presumably complete gene sets for NADH:quinone oxidoreductase (complex I) were identified in the genome and there is evidence that either NADH or reduced ferredoxin might serve as electron donor. Beside the typical archaeal A0A1-ATP synthase, a membrane-bound pyrophosphatase is found, which might contribute to energy conservation. Surprisingly, all genes required for dissimilatory sulfate reduction are present, which is confirmed by growth experiments. Mentionable is furthermore, the presence of two proteins (ParA family ATPase, actin-like protein) that might be involved in cell division in Thermoproteales, where the ESCRT system is absent, and of genes involved in genetic competence (DprA, ComF) that is so far unique within Archaea.

TinyVM: an energy‐efficient execution infrastructure for sensor networks

SUMMARYEnergy‐efficient implementation techniques for virtual machines (VMs) have received little attention yet: conventional wisdom claims that VMs have a diametrical effect on energy consumption, and VM‐based applications are therefore short‐lived. In this paper, we argue that bytecode interpretation is affordable if we synthesize VMs specifically for energy efficiency. We present TinyVM, an execution infrastructure that seamlessly integrates with C and nesC/TinyOS‐based programming environments. TinyVM achieves high code density through the use of compressed bytecode as the primary program representation. Compressed bytecode allows rapid application deployment with low communication overhead. TinyVM executes compressed bytecode in place, which eliminates the need for a decompression stage and thereby reduces memory consumption on sensor nodes. Our infrastructure automates the creation of energy‐efficient application‐specific VMs. Applications are partitioned in machine code, bytecode, and VM instruction set extensions. Partitioning is manually controlled and/or fully guided by a discrete optimization problem that produces a partitioning with lowest energy consumption for a given program size limit. We provide experimental results for sensor network benchmarks and for selected applications on various CPU architectures including Atmega128‐based motes and the ARM‐based Intel iMote2. TinyVM has been released under the GNU General Public License. Copyright © 2011 John Wiley & Sons, Ltd.

Genome analyses and modelling the relationships between coding density, recombination rate and chromosome length

In the human genomes, recombination frequency between homologous chromosomes during meiosis is highly correlated with their physical length while it differs significantly when their coding density is considered. Furthermore, it has been observed that the recombination events are distributed unevenly along the chromosomes. We have found that many of such recombination properties can be predicted by computer simulations of population evolution based on the Monte Carlo methods. For example, these simulations have shown that the probability of acceptance of the recombination events by selection is higher at the ends of chromosomes and lower in their middle parts. The regions of high coding density are more prone to enter the strategy of haplotype complementation and to form clusters of genes, which are “recombination deserts”. The phenomenon of switching in-between the purifying selection and haplotype complementation has a phase transition character, and many relations between the effective population size, coding density, chromosome size and recombination frequency are those of the power law type.

Architecture Design of a Variable Length Instruction Set VLIW DSP

The cost of the central register file and the size of the program code limit the scalability of very long instruction word (VLIW) processors with increasing numbers of functional units. This paper presents the architectural design of a six-way VLIW digital signal processor (DSP) with clustered register files. The architecture uses a variable length instruction set and supports dynamic instruction dispatching. The one-level memory system architecture of the processor includes 16-KB instruction and data caches and 16-KB instruction and data on-chip RAM. A compiler based on the Open64 was developed for the system. Evaluations show that the processor is suitable for high performance applications with a high code density and small program code size.

The 160-Kilobase Genome of the Bacterial Endosymbiont Carsonella

Previous studies have suggested that the minimal cellular genome could be as small as 400 kilobases. Here, we report the complete genome sequence of the psyllid symbiont Carsonella ruddii, which consists of a circular chromosome of 159,662 base pairs, averaging 16.5% GC content. It is by far the smallest and most AT-rich bacterial genome yet characterized. The genome has a high coding density (97%) with many overlapping genes and reduced gene length. Genes for translation and amino acid biosynthesis are relatively well represented, but numerous genes considered essential for life are missing, suggesting that Carsonella may have achieved organelle-like status.

AE32000B: a Fully Synthesizable 32-Bit Embedded Microprocessor Core

In this paper, we introduce a fully synthesizable 32-bit embedded microprocessor core called the AE32000B. The AE32000B core is based on the extendable instruction set computer architecture, so it has high code density and a low memory access rate. In order to improve the performance of the core, we developed and adopted various design options, including the load extension register instruction (LERI) folding unit, a high performance multiply and accumulate (MAC) unit, various DSP units, and an efficient coprocessor interface. The instructions per cycle count of the Dhrystone 2.1 benchmark for the designed core is about 0.86. We verified the synthesizability and the area and time performances of our design using two CMOS standard cell libraries: a 0.35-·m library and a 0.18-·m library. With the 0.35-·m library, the core can be synthesized with about 47,000 gates and operate at 70 MHz or higher, while it can be synthesized with about 53,000 gates and operate at 120 MHz or higher with the 0.18-·m library.

A Survey of the Genome of the Hyperthermophilic Archaeon,Pyrococcus furiosus

Pyrococcus furiosus is a marine microorganism with the unusual ability to grow optimally at 100°C. It is classified as a member of the domain Archaea (Archaebacteria). We present studies on the genome of P. furiosus, consisting of a precise determination of the size of the chromosome, 2.05 mb, and an analysis of sequence data from cDNA and genomic libraries. The sequence analysis included a total of 1176 sequences, representing 14.7% of the genome, which were compared with the current databases using the BLAST X algorithm. Expressed sequence tag (EST) analysis is skewed toward the repeated detection of highly expressed genes, for example, ribosomal RNA, in P. furiosus. The relatively small size of the genome implies a high coding density, and randomly chosen genomic sequences provide good performance in gene discovery with relatively fewer identical hits compared with the EST database. The recovery of database matches with P(n) ≤ 1.0e−05 was 30% of the total sequences tested. We estimate that the genome contains approximately 1800 genes, and this study has provided evidence for 309 genes. The average G+C content of the sequences obtained was 41.2%, and no repetitive sequences were detected. Genes from Eukarya and Bacteria are almost equally represented in the matches obtained in this study. The homologs representing central metabolism exhibit preferential similarity to their homologs from bacteria, despite the availability of eukaryotic homologs in the databases. Several characteristically eukaryotic protein homologs were found with functions in transcription, translation, and membrane transport. We propose that the archaeal genome is a mosaic, consisting of ancient gene sequences related to eukaryal homologs and more recently acquired genes, many of which are related to bacterial metabolic functions. Further sequencing and phylogenetic studies are needed to confirm this hypothesis, which predicts that there was extensive lateral genetic transfer among Bacteria, Eukarya, and Archaea during a period when the original gene pool was expanding into the early lineages of life.

SH3: high code density, low power

Hitachi's SH series microprocessors feature 32-bit RISC architecture with a 16-bit, fixed-length instruction set. We describe SH3, a pipelined implementation of the SH architecture with on-chip cache, MMU, and software-programmable power management. Its higher code density and corresponding improvement in instruction-fetch latency lead to higher performance than typical 32-bit RISC architectures achieve. These features, small die size, and low power consumption make SH3 an ideal microprocessor for portable computing systems or multimedia systems.