Genomic imprints of unparalleled growth

Chlorella ohadii was isolated from desert biological soil crusts, one of the harshest habitats on Earth, and is emerging as an exciting new green model for studying growth, photosynthesis and metabolism under a wide range of conditions. Here, we compared the genome of C. ohadii, the fastest growing alga on record, to that of other green algae, to reveal the genomic imprints empowering its unparalleled growth rate and resistance to various stressors, including extreme illumination. This included the genome of its close relative, but slower growing and photodamage sensitive, C. sorokiniana UTEX 1663. A larger number of ribosome-encoding genes, high intron abundance, increased codon bias and unique genes potentially involved in metabolic flexibility and resistance to photodamage are all consistent with the faster growth of C. ohadii. Some of these characteristics highlight general trends in Chlorophyta and Chlorella spp. evolution, and others open new broad avenues for mechanistic exploration of their relationship with growth. This work entails a unique case study for the genomic adaptations and costs of exceptionally fast growth and sheds light on the genomic signatures of fast growth in photosynthetic cells. It also provides an important resource for future studies leveraging the unique properties of C. ohadii for photosynthesis and stress response research alongside their utilization for synthetic biology and biotechnology aims.

Transcriptional up-regulation of host-specific terpene metabolism in aphid-induced galls of Pistacia palaestina

Galling insects gain food and shelter by inducing specialized anatomical structures in their plant hosts. Such galls often accumulate plant defensive metabolites protecting the inhabiting insects from predation. We previously found that, despite a marked natural chemopolymorphism in natural populations of Pistacia palaestina, the monoterpene content in Baizongia pistaciae-induced galls is substantially higher than in leaves of their hosts. Here we show a general up-regulation of key structural genes in both the plastidial and cytosolic terpene biosynthetic pathways in galls as compared with non-colonized leaves. Novel prenyltransferases and terpene synthases were functionally expressed in Escherichia coli to reveal their biochemical function. Individual Pistacia trees exhibiting chemopolymorphism in terpene compositions displayed differential up-regulation of selected terpene synthase genes, and the metabolites generated by their gene products in vitro corresponded to the monoterpenes accumulated by each tree. Our results delineate molecular mechanisms responsible for the formation of enhanced monoterpene in galls and the observed intraspecific monoterpene chemodiversity displayed in P. palaestina. We demonstrate that gall-inhabiting aphids transcriptionally reprogram their host terpene pathways by up-regulating tree-specific genes, boosting the accumulation of plant defensive compounds for the protection of colonizing insects.

Factors Enhancing the Antibacterial Effect of Monovalent Copper Ions

This study continues the series of experiments that demonstrate the high antibacterial properties of monovalent copper ions (Cu⁺). While in previous study we examined different metals (copper and silver) and their metal states (mono- and divalent), showing that monovalent copper is best for controlling bacterial growth, the current study focuses on finding conditions which further enhance the antibacterial effect of monovalent copper. This approach may also shed light on mechanisms of Cu⁺ ions which still remain unknown. To this end, the influence of Cu⁺ ions on model gram-negative Escherichia coli bacteria at different pH levels with a variety of carbon sources and elevated temperatures was examined. It was found that in both aerobic and anaerobic conditions in a poor growth medium, Cu²⁺ ions barely suppress any growth of E. coli, whereas Cu⁺ ions even at very low concentrations dramatically deplete bacterial populations in a time scale of minutes at room temperature, and less than one minute at elevated temperatures. Acidic pH, unfavorable carbon sources, and elevated temperatures boost the antibacterial action of Cu⁺ ions. On the whole, the study confirms that monovalent copper ions are strongly superior to divalent copper ions in their antibacterial action across a wide range of tested conditions.

Resequencing of a mutant bearing an iron starvation recovery phenotype defines Slr1658 as a new player in the regulatory network of a model cyanobacterium

Photosynthetic microorganisms encounter an erratic nutrient environment characterized by periods of iron limitation and sufficiency. Surviving in such an environment requires mechanisms for handling these transitions. Our study identified a regulatory system involved in the process of recovery from iron limitation in cyanobacteria. We set out to study the role of bacterioferritin co-migratory proteins during transitions in iron bioavailability in the cyanobacterium Synechocystis sp. PCC 6803 using knockout strains coupled with physiological and biochemical measurements. One of the mutants displayed slow recovery from iron limitation. However, we discovered that the cause of the phenotype was not the intended knockout but rather the serendipitous selection of a mutation in an unrelated locus, slr1658. Bioinformatics analysis suggested similarities to two-component systems and a possible regulatory role. Transcriptomic analysis of the recovery from iron limitation showed that the slr1658 mutation had an extensive effect on the expression of genes encoding regulatory proteins, proteins involved in the remodeling and degradation of the photosynthetic apparatus and proteins modulating electron transport. Most significantly, expression of the cyanobacterial homologue of the cyclic electron transport protein PGR5 was upregulated 1000-fold in slr1658 disruption mutants. pgr5 transcripts in the Δslr1658 mutant retained these high levels under a range of stress and recovery conditions. The results suggest that slr1658 is part of a regulatory operon that, among other aspects, affects the regulation of alternative electron flow. Disruption of its function has deleterious results under oxidative stress promoting conditions.

Prevalence of Monovalent Copper Over Divalent in Killing Escherichia coli and Staphylococcus aureus

This study opens the investigation series focused on antimicrobial effects of copper (Cu) compared to silver (Ag), which is currently used to treat wound infection in burn victims as well as in chronic wounds. Noticeably, in its ionized state, Cu is more commonly present as Cu²⁺ rather than as Cu⁺, while electronic configuration similarity of Cu⁺ and Ag⁺ indicates that actually it may be the active state. To test this hypothesis, effect of Cu⁺ and Cu²⁺, using Ag⁺ ions and metallic copper as controls on Escherichia coli and Staphylococcus aureus bacteria, was examined under anaerobic conditions. Cu⁺ was produced by two different methods, and its effect on microorganism growth was tested using a syringe and Petri dish methods. It was found that the presence of Cu⁺ causes a dramatic depletion in the viability of both microorganisms. Metallic copper did not have any effect on the viability, whereas Cu²⁺ and Ag⁺ ions had much lower activity than Cu⁺ ions. Minimal inhibitory concentration of Cu⁺ for E. coli was twice lower than that of Cu²⁺. The obtained results show that Cu⁺ proves to be a potent antimicrobial agent.

What distinguishes cyanobacteria able to revive after desiccation from those that cannot: the genome aspect

Filamentous cyanobacteria are the main founders and primary producers in biological desert soil crusts (BSCs) and are likely equipped to cope with one of the harshest environmental conditions on earth including daily hydration/dehydration cycles, high irradiance and extreme temperatures. Here, we resolved and report on the genome sequence of Leptolyngbya ohadii, an important constituent of the BSC. Comparative genomics identified a set of genes present in desiccation-tolerant but not in dehydration-sensitive cyanobacteria. RT qPCR analyses showed that the transcript abundance of many of them is upregulated during desiccation in L. ohadii. In addition, we identified genes where the orthologs detected in desiccation-tolerant cyanobacteria differs substantially from that found in desiccation-sensitive cells. We present two examples, treS and fbpA (encoding trehalose synthase and fructose 1,6-bisphosphate aldolase respectively) where, in addition to the orthologs present in the desiccation-sensitive strains, the resistant cyanobacteria also possess genes with different predicted structures. We show that in both cases the two orthologs are transcribed during controlled dehydration of L. ohadii and discuss the genetic basis for the acclimation of cyanobacteria to the desiccation conditions in desert BSC.

The mechanisms whereby the green alga Chlorella ohadii, isolated from desert soil crust, exhibits unparalleled photodamage resistance

Excess illumination damages the photosynthetic apparatus with severe implications with regard to plant productivity. Unlike model organisms, the growth of Chlorella ohadii, isolated from desert soil crust, remains unchanged and photosynthetic O2 evolution increases, even when exposed to irradiation twice that of maximal sunlight. Spectroscopic, biochemical and molecular approaches were applied to uncover the mechanisms involved. D1 protein in photosystem II (PSII) is barely degraded, even when exposed to antibiotics that prevent its replenishment. Measurements of various PSII parameters indicate that this complex functions differently from that in model organisms and suggest that C. ohadii activates a nonradiative electron recombination route which minimizes singlet oxygen formation and the resulting photoinhibition. The light-harvesting antenna is very small and carotene composition is hardly affected by excess illumination. Instead of succumbing to photodamage, C. ohadii activates additional means to dissipate excess light energy. It undergoes major structural, compositional and physiological changes, leading to a large rise in photosynthetic rate, lipids and carbohydrate content and inorganic carbon cycling. The ability of C. ohadii to avoid photodamage relies on a modified function of PSII and the dissipation of excess reductants downstream of the photosynthetic reaction centers. The biotechnological potential as a gene source for crop plant improvement is self-evident.

Insight into glucosidase II from the red marine microalga Porphyridium sp. (Rhodophyta)

N-glycosylation of proteins is one of the most important post-translational modifications that occur in various organisms, and is of utmost importance for protein function, stability, secretion, and loca-lization. Although the N-linked glycosylation pathway of proteins has been extensively characterized in mammals and plants, not much information is available regarding the N-glycosylation pathway in algae. We studied the α 1,3-glucosidase glucosidase II (GANAB) glycoenzyme in a red marine microalga Porphyridium sp. (Rhodophyta) using bioinformatic and biochemical approaches. The GANAB-gene was found to be highly conserved evolutionarily (compo-sed of all the common features of α and β subunits) and to exhibit similar motifs consistent with that of homolog eukaryotes GANAB genes. Phylogenetic analysis revealed its wide distribution across an evolutionarily vast range of organisms; while the α subunit is highly conserved and its phylogenic tree is similar to the taxon evolutionary tree, the β subunit is less conserved and its pattern somewhat differs from the taxon tree. In addition, the activity of the red microalgal GANAB enzyme was studied, including functional and biochemical characterization using a bioassay, indicating that the enzyme is similar to other eukaryotes ortholog GANAB enzymes. A correlation between polysaccharide production and GANAB activity, indicating its involvement in polysaccharide biosynthesis, is also demonstrated. This study represents a valuable contribution toward understanding the N-glycosylation and polysaccharide biosynthesis pathways in red microalgae.

Generation and annotation of the DNA sequences of human chromosomes 2 and 4

Human chromosome 2 is unique to the human lineage in being the product of a head-to-head fusion of two intermediate-sized ancestral chromosomes. Chromosome 4 has received attention primarily related to the search for the Huntington's disease gene, but also for genes associated with Wolf-Hirschhorn syndrome, polycystic kidney disease and a form of muscular dystrophy. Here we present approximately 237 million base pairs of sequence for chromosome 2, and 186 million base pairs for chromosome 4, representing more than 99.6% of their euchromatic sequences. Our initial analyses have identified 1,346 protein-coding genes and 1,239 pseudogenes on chromosome 2, and 796 protein-coding genes and 778 pseudogenes on chromosome 4. Extensive analyses confirm the underlying construction of the sequence, and expand our understanding of the structure and evolution of mammalian chromosomes, including gene deserts, segmental duplications and highly variant regions.

EAnnot: a genome annotation tool using experimental evidence

The sequence of any genome becomes most useful for biological experimentation when a complete and accurate gene set is available. Gene prediction programs offer an efficient way to generate an automated gene set. Manual annotation, when performed by experienced annotators, is more accurate and complete than automated annotation. However, it is a laborious and expensive process, and by its nature, introduces a degree of variability not found with automated annotation. EAnnot (Electronic Annotation) is a program originally developed for manually annotating the human genome. It combines the latest bioinformatics tools to extract and analyze a wide range of publicly available data in order to achieve fast and reliable automatic gene prediction and annotation. EAnnot builds gene models based on mRNA, EST, and protein alignments to genomic sequence, attaches supporting evidence to the corresponding genes, identifies pseudogenes, and locates poly(A) sites and signals. Here, we compare manual annotation of human chromosome 6 with annotation performed by EAnnot in order to assess the latter's accuracy. EAnnot can readily be applied to manual annotation of other eukaryotic genomes and can be used to rapidly obtain an automated gene set.

The Salmonella SpiC protein targets the mammalian Hook3 protein function to alter cellular trafficking

The Salmonella SpiC protein is secreted into the cytosol of macrophages via a unique type III secretion system that functions intracellularly to translocate proteins across the phagosomal membrane. The SpiC protein is required for survival within macrophages and inhibition of phagosome-lysosome fusion in vivo, and it is sufficient to inhibit endosome-endosome fusion in vitro. Here, we establish that SpiC targets the function of Hook3, a mammalian protein implicated in cellular trafficking. Purified GST-SpiC pulled down Hook3 from murine macrophages, and anti-Hook3 antibodies precipitated SpiC from the cytosol of Salmonella-infected macrophages. Expression of the spiC gene disrupted Golgi morphology in Vero cells and altered the distribution of lysosomes in macrophages, mimicking the phenotype of cells expressing a hook3 dominant-negative mutant. By inactivating Hook3 function, the SpiC protein may alter the lysosome network and prevent phagosome-lysosome fusion.

[Screening for early detection of prostate cancer (first experience in Israel)]

Prostatic cancer (PC) is second only to lung cancer as a cause of cancer mortality in men word-wide. In Israel it is the most common cause of cancer mortality in men, after lung cancer and colo-rectal cancer. We screened, for the first time in Israel, for prostatic cancer using serum levels of PSA and a digital rectal examination (DRE). The purpose was not only to diagnose PC but also to increase public awareness of the condition. 300 men in the Haifa area who met statistical criteria for early diagnosis of PC participated. They filled a questionnaire regarding risk factors for PC (age, family history (FH) of prostatic and breast cancer, cigarette smoking, alcohol consumption, previous PSA sampling) and were examined. Those who had out-of-range, age-related PSA values, or a pathologic DRE underwent trans-rectal ultrasound (TRUS) examination and guided biopsy of the prostate. Those with a positive biopsy for PC underwent radical prostatectomy or radiation therapy. 41 (14.3%) had out-of-range, age-related PSA levels and 10 (3.5%) had a pathologic DRE. 39 (13.3%) underwent TRUS and biopsy and 6 (2.04%) had clinically significant PC, all early stages (Gleason 4-6). Correlation between age and PSA has been proven statistically significant (p < 0.05). Symptoms of urinary tract obstruction and nocturia were related to a high PSA (p = 0.035 and 0.002, respectively). Those with PC had at least 1 symptom of urinary tract obstruction; 6 (15.3%) who underwent TRUS and biopsy and a FH of prostate cancer. However, no subject with a FH of PC had biopsy-proven cancer. Those with PC had PSA values from 4.9 to 31.8 ng/ml (9.6 median). Age-related PSA had a positive predictive value of 17.1%. Results of our annual screening for early detection of PC using age-related PSA, and DRE are encouraging: cases detected were clinically significant and treatable. It would appear that screening for PC will result in decreasing the incidence of metastatic cancer and therefore mortality.

Characterization of a conserved alpha-helical, coiled-coil motif at the C-terminal domain of the ATP-dependent FtsH (HflB) protease of Escherichia coli

FtsH (HflB) is an ATP-dependent protease found in prokaryotic cells, mitochondria and chloroplasts. Here, we have identified, in the carboxy-terminal region of FtsH (HfIB), a short alpha helix predicted of forming a coiled-coil, leucine zipper, structure. This region appears to be structurally conserved. The presence of the coiled-coil motif in the Escherichia coli FtsH (HflB) was demonstrated by circular dichroism and cross-linking experiments. Mutational analysis showed that three highly conserved leucine residues are essential for FtsH (HfIB) activity in vivo and in vitro. Purified proteins mutated in the conserved leucine residues, were found to be defective in the degradation of E. coli sigma(32) and the bacteriophage lambda CII proteins. In addition, the mutant proteins were defective in the binding of CII The mutations did not interfere with the ATPase activity of FtsH (HflB). Finally, the mutant proteins were found to be more sensitive to trypsin degradation than the wild-type enzyme suggesting that the alpha helical region is an important structural element of FtsH (HflB).

Proteolysis of bacteriophage lambda CII by Escherichia coli FtsH (HflB)

FtsH (HflB) is a conserved, highly specific, ATP-dependent protease for which a number of substrates are known. The enzyme participates in the phage lambda lysis-lysogeny decision by degrading the lambda CII transcriptional activator and by its response to inhibition by the lambda CIII gene product. In order to gain further insight into the mechanism of the enzymatic activity of FtsH (HflB), we identified the peptides generated following proteolysis of the phage lambda CII protein. It was found that FtsH (HflB) acts as an endopeptidase degrading CII into small peptides with limited amino acid specificity at the cleavage site. beta-Casein, an unstructured substrate, is also degraded by FtsH (HflB), suggesting that protein structure may play a minor role in determining the products of proteolysis. The majority of the peptides produced were 13 to 20 residues long.

A colicin-tolerant Escherichia coli mutant that confers hfl phenotype carries two mutations in the region coding for the C-terminal domain of FtsH (HflB)

An Escherichia coli mutant, ER437, which was originally isolated for colicin tolerance, was found to carry two amino acid changes in the C-terminal portion of FtsH (HflB). These mutations were demonstrated to reduce the ability of FtsH to degrade the phage lambda CII protein in vivo and in vitro, providing a rationalization for the mutant Hfl phenotype.

Stability of CII is a key element in the cold stress response of bacteriophage lambda infection

Bacteria are known to adapt to environmental changes such as temperature fluctuations. It was found that temperature affects the lysis-lysogeny decision of lambda such that at body temperature (37 degrees C) the phage can select between the lytic and lysogenic pathways, while at ambient temperature (20 degrees C) the lytic pathway is blocked. This temperature-dependent discriminatory developmental pathway is governed mainly by the phage CII activity as a transcriptional activator. Mutations in cII or point mutations at the pRE promoter lead to an over-1,000-fold increase in mature-phage production at low temperature while mutations in cI cause a smaller increase in phage production. Interference with CII activity can restore lytic growth at low temperature. We found that at low temperature the stability of CII in vivo is greatly increased. It was also found that phage DNA replication is blocked at 20 degrees C but can be restored by supplying O and P in trans. It is proposed that CII hampers transcription of the rightward pR promoter, thus reducing the levels of the lambda O and P proteins, which are necessary for phage DNA replication. Our results implicate CII itself or host proteins affecting CII stability as a "molecular thermometer".

Proteolysis of the phage lambda CII regulatory protein by FtsH (HflB) of Escherichia coli

Rapid proteolysis plays an important role in regulation of gene expression. Proteolysis of the phage lambda CII transcriptional activator plays a key role in the lysis-lysogeny decision by phage lambda. Here we demonstrate that the E. coli ATP-dependent protease FtsH, the product of the host ftsH/hflB gene, is responsible for the rapid proteolysis of the CII protein. FtsH was found previously to degrade the heat-shock transcription factor sigma32. Proteolysis of sigma32 requires, in vivo, the presence of the DnaK-DnaJ-GrpE chaperone machine. Neither DnaK-DnaJ-GrpE nor GroEL-GroES chaperone machines are required for proteolysis of CII in vivo. Purified FtsH carries out specific ATP-dependent proteolysis of CII in vitro. The degradation of CII is at least 10-fold faster than that of sigma32. Electron microscopy revealed that purified FtsH forms ring-shaped structures with a diameter of 6-7 nm.

Electroejaculation and assisted fertility in men with psychogenic anejaculation

OBJECTIVES

To evaluate sperm characteristics and fertility potential in ejaculates obtained after electroejaculation in men with psychogenic anejaculation.

DESIGN

Retrospective clinical study.

SETTING

In Vitro Fertilization Unit, Bikur Cholim Hospital, Jerusalem, Israel.

PATIENTS

Twenty men with psychogenic anejaculation who underwent 55 sessions of electroejaculation and their spouses.

INTERVENTIONS

Electroejaculation, assisted reproduction technologies.

MAIN OUTCOME MEASURES

Semen analysis, IVF, intracytoplasmic injection (ICSI), fertilization rates, and pregnancy rates.

RESULTS

In all patients, sperm density and motility rates were unsatisfactory (98 +/- 127 x 10(6) with 14.6% +/- 15% motility in the antegrade portions and 42 +/- 42 x 10(6) with 9.7% +/- 15.6% motility in the retrograde samples). Intrauterine inseminations performed in eight couples did not result in a pregnancy. Four couples underwent IVF-ET treatments. Two pregnancies were achieved with overall success rates of 22% per cycle. Five couples were treated using the ICSI procedure. Although good quality embryos were transferred, none of the treatments resulted in a pregnancy.

CONCLUSIONS

Psychogenic failure to ejaculate may be treated by electroejaculation. However, the average motility of the sperm obtained is diminished. The combination of electroejaculation with IVF, including the ICSI procedure, should improve chances of fertilization and pregnancy in these cases.

Malleable penile prosthesis removal leaving behind the rear tip extenders: a clinical presentation

Perineal pain and a foreign body in a scout abdominal X-ray are reported as presenting symptoms of a patient who later gave an anamnesis of a penile prosthesis implantation which had become infected and was removed. The foreign bodies turned out to be two rear tip extenders of the prosthesis left behind causing the perineal pain.

Comparison of penile duplex ultrasonography with nocturnal penile tumescence monitoring for the evaluation of erectile impotence

A total of 50 patients with erectile dysfunction underwent comprehensive evaluation, including vascular evaluation with penile duplex ultrasonography and papaverine injection, as well as nocturnal penile tumescence monitoring. The latter was performed in a sleep laboratory setting in all patients. The results of penile duplex ultrasonography with papaverine injection were classified as 18 patients with normal vascular findings, 22 with arterial insufficiency, 3 with the pelvic steal syndrome and 7 with isolated venous leakage. Of the patients 15 had normal ultrasonographic and nocturnal penile tumescence findings, 29 had abnormal ultrasonographic vascular and nocturnal penile tumescence findings, 3 had abnormal ultrasonographic vascular findings and normal nocturnal penile tumescence (including 1 with the pelvic steal syndrome as evidenced by penile brachial index) and 3 had normal ultrasonographic vascular findings and abnormal nocturnal penile tumescence (including 2 with neurogenic erectile dysfunction). Penile duplex ultrasonography with papaverine injection appears to be a useful objective method to evaluate vasculogenic impotence and to correlate favorably with nocturnal penile tumescence monitoring. It also may have a higher yield than nocturnal penile tumescence monitoring in patients with the pelvic steal syndrome. While nocturnal penile tumescence is impaired in patients with neurogenic impotence, penile duplex ultrasonography with papaverine injection reveals, as expected, normal findings in patients with neurogenic impotence and normal vascular systems.